├── .editorconfig ├── .github ├── ISSUE_TEMPLATE.md └── PULL_REQUEST_TEMPLATE.md ├── .gitignore ├── .gitmodules ├── .travis.yml ├── AUTHORS.rst ├── CONTRIBUTING.rst ├── HISTORY.rst ├── LICENSE ├── MANIFEST.in ├── Makefile ├── README.rst ├── codecov.yml ├── conda_requirements.txt ├── docs ├── CHANGELOG_sphinx_deployment.md ├── LICENSE_sphinx_deployment ├── Makefile ├── README_sphinx_deployment.md ├── _static │ ├── exon_vs_junction_start_stop.ai │ ├── outrigger_franken-events.ai │ ├── outrigger_index-150ppi.png │ ├── outrigger_index-1x.png │ ├── outrigger_index-300ppi.png │ ├── outrigger_index.ai │ ├── outrigger_index.svg │ ├── outrigger_index_flanking_exons.ai │ ├── outrigger_index_mxe.ai │ ├── outrigger_index_se.ai │ ├── outrigger_overview-150ppi.png │ ├── outrigger_overview-1x.png │ ├── outrigger_overview-300ppi.png │ ├── outrigger_overview_v1.ai │ ├── outrigger_overview_v1.svg │ ├── outrigger_overview_v2.ai │ ├── outrigger_psi-150ppi.png │ ├── outrigger_psi-1x.png │ ├── outrigger_psi-300ppi.png │ ├── outrigger_psi_pathological_cases.ai │ ├── outrigger_psi_v1.ai │ ├── outrigger_psi_v2.ai │ ├── outrigger_psi_v3.ai │ ├── outrigger_validate-150ppi.png │ ├── outrigger_validate-1x.png │ ├── outrigger_validate-300ppi.png │ ├── outrigger_validate.ai │ └── outrigger_validate.svg ├── authors.rst ├── conf.py ├── contributing.rst ├── history.rst ├── index.rst ├── installation.rst ├── make.bat ├── releases │ ├── checklist.md │ ├── template.rst │ ├── v0.1.0.rst │ ├── v0.2.0.rst │ ├── v0.2.1.rst │ ├── v0.2.2.rst │ ├── v0.2.3.rst │ ├── v0.2.4.rst │ ├── v0.2.5.rst │ ├── v0.2.6.rst │ ├── v0.2.7.rst │ ├── v0.2.8.rst │ ├── v0.2.9.rst │ ├── v1.0.0.rst │ └── v1.1.0.rst ├── requirements.txt ├── rsync_exclude ├── sphinx_deployment.mk ├── subcommands │ ├── outrigger_index.rst │ ├── outrigger_psi.rst │ └── outrigger_validate.rst ├── test_transcripts.png ├── tutorial.rst └── usage.rst ├── environment.yml ├── logo ├── logo-150ppi.png ├── logo-1x.png ├── logo-300ppi.png ├── logo.ai └── logo.svg ├── make_test_data.ipynb ├── meta.yml ├── outrigger ├── __init__.py ├── commandline.py ├── common.py ├── index │ ├── __init__.py │ ├── adjacencies.py │ └── events.py ├── io │ ├── __init__.py │ ├── bam.py │ ├── core.py │ ├── gtf.py │ └── star.py ├── psi │ ├── __init__.py │ └── compute.py ├── region.py ├── tests │ ├── __init__.py │ ├── conftest.py │ ├── data │ │ ├── arabdopsis │ │ │ └── unprocessed │ │ │ │ ├── Arabidopsis_thaliana.TAIR10.31.chr4.gtf │ │ │ │ ├── Arabidopsis_thaliana.TAIR10.31.chr4.subset.gtf │ │ │ │ ├── rna.chr4.SJ.out.tab │ │ │ │ └── rna.chr4.subset.SJ.out.tab │ │ ├── simulated │ │ │ ├── outrigger_output │ │ │ │ └── index │ │ │ │ │ ├── mxe │ │ │ │ │ ├── events_negative_strand.csv │ │ │ │ │ └── events_positive_strand.csv │ │ │ │ │ └── se │ │ │ │ │ ├── events_negative_strand.csv │ │ │ │ │ └── events_positive_strand.csv │ │ │ ├── psi │ │ │ │ ├── mutually_exclusive_exon_junctions_psi.csv │ │ │ │ └── skipped_exon_junctions_psi.csv │ │ │ ├── unprocessed │ │ │ │ └── true_splice_junctions.csv │ │ │ └── validate_negative_control │ │ │ │ ├── chromsizes │ │ │ │ ├── exon2_downstream_splice_sites.csv │ │ │ │ ├── exon2_upstream_splice_sites.csv │ │ │ │ ├── genome.docx │ │ │ │ ├── genome.fasta │ │ │ │ ├── genome.fasta.fai │ │ │ │ ├── outrigger_output │ │ │ │ └── index │ │ │ │ │ ├── mxe │ │ │ │ │ ├── events.csv │ │ │ │ │ ├── exon1.bed │ │ │ │ │ ├── exon2.bed │ │ │ │ │ ├── exon3.bed │ │ │ │ │ ├── exon4.bed │ │ │ │ │ ├── splice_sites.csv │ │ │ │ │ └── validated │ │ │ │ │ │ └── events.csv │ │ │ │ │ └── se │ │ │ │ │ ├── events.csv │ │ │ │ │ ├── exon1.bed │ │ │ │ │ ├── exon2.bed │ │ │ │ │ ├── exon3.bed │ │ │ │ │ ├── splice_sites.csv │ │ │ │ │ └── validated │ │ │ │ │ └── events.csv │ │ │ │ └── ~$genome.docx │ │ ├── tasic2016 │ │ │ ├── intermediate │ │ │ │ ├── adjacent_junctions_single_exon.csv │ │ │ │ ├── bam │ │ │ │ │ ├── CAV_LP_Ipsi_tdTpos_cell_1-SRR2140356-GSM1840944_R1.polyATrim.adapterTrim.rmRep.sorted.rg.subset.sorted.bam.outrigger_junction_reads_ignore-multimappingFalse.csv │ │ │ │ │ ├── CAV_LP_Ipsi_tdTpos_cell_1-SRR2140356-GSM1840944_R1.polyATrim.adapterTrim.rmRep.sorted.rg.subset.sorted.bam.outrigger_junction_reads_ignore-multimappingTrue.csv │ │ │ │ │ ├── CAV_LP_Ipsi_tdTpos_cell_1-SRR2140356-GSM1840944_R1.polyATrim.adapterTrim.rmRep.sorted.rg.subset.sorted.junction_reads_ignore-multimappingFalse.csv │ │ │ │ │ ├── CAV_LP_Ipsi_tdTpos_cell_1-SRR2140356-GSM1840944_R1.polyATrim.adapterTrim.rmRep.sorted.rg.subset.sorted.junction_reads_ignore-multimappingFalse_empty_multi.csv │ │ │ │ │ ├── CAV_LP_Ipsi_tdTpos_cell_1-SRR2140356-GSM1840944_R1.polyATrim.adapterTrim.rmRep.sorted.rg.subset.sorted.junction_reads_ignore-multimappingFalse_empty_uniquely.csv │ │ │ │ │ ├── CAV_LP_Ipsi_tdTpos_cell_1-SRR2140356-GSM1840944_R1.polyATrim.adapterTrim.rmRep.sorted.rg.subset.sorted.junction_reads_ignore-multimappingTrue.csv │ │ │ │ │ ├── CAV_LP_Ipsi_tdTpos_cell_1-SRR2140356-GSM1840944_R1.polyATrim.adapterTrim.rmRep.sorted.rg.subset.sorted.junction_reads_ignore-multimappingTrue_empty_multi.csv │ │ │ │ │ ├── CAV_LP_Ipsi_tdTpos_cell_1-SRR2140356-GSM1840944_R1.polyATrim.adapterTrim.rmRep.sorted.rg.subset.sorted.junction_reads_ignore-multimappingTrue_empty_uniquely.csv │ │ │ │ │ ├── CAV_LP_Ipsi_tdTpos_cell_1-SRR2140356-GSM1840944_R1.polyATrim.adapterTrim.rmRep.sorted.rg.subset.sorted.junction_reads_multimapped.csv │ │ │ │ │ ├── CAV_LP_Ipsi_tdTpos_cell_1-SRR2140356-GSM1840944_R1.polyATrim.adapterTrim.rmRep.sorted.rg.subset.sorted.junction_reads_uniquelymapped.csv │ │ │ │ │ ├── CAV_LP_Ipsi_tdTpos_cell_1-SRR2140356-GSM1840944_R1.polyATrim.adapterTrim.rmRep.sorted.rg.subset.sorted.uniquely_mapped_summed.csv │ │ │ │ │ ├── CAV_LP_Ipsi_tdTpos_cell_2-SRR2140357-GSM1840945_R1.polyATrim.adapterTrim.rmRep.sorted.rg.subset.sorted.bam.outrigger_junction_reads_ignore-multimappingFalse.csv │ │ │ │ │ └── CAV_LP_Ipsi_tdTpos_cell_2-SRR2140357-GSM1840945_R1.polyATrim.adapterTrim.rmRep.sorted.rg.subset.sorted.bam.outrigger_junction_reads_ignore-multimappingTrue.csv │ │ │ │ ├── index │ │ │ │ │ └── star │ │ │ │ │ │ ├── splice_junctions_ignore_multimappingFalse.csv │ │ │ │ │ │ └── splice_junctions_ignore_multimappingTrue.csv │ │ │ │ ├── junction_metadata.csv │ │ │ │ ├── junctions_genome_adjacent_downstream.csv │ │ │ │ ├── junctions_genome_adjacent_to_exon_downstream.csv │ │ │ │ ├── junctions_genome_adjacent_to_exon_upstream.csv │ │ │ │ ├── junctions_genome_adjacent_upstream.csv │ │ │ │ ├── neighboring_exons.csv │ │ │ │ ├── psi │ │ │ │ │ ├── mxe │ │ │ │ │ │ └── summary.csv │ │ │ │ │ ├── mxe_event_df.csv │ │ │ │ │ ├── se │ │ │ │ │ │ └── summary.csv │ │ │ │ │ ├── se_event_df.csv │ │ │ │ │ └── splice_junction_reads.csv │ │ │ │ └── single_junction_exon_triple.csv │ │ │ ├── outrigger_output │ │ │ │ ├── index │ │ │ │ │ ├── exon_direction_junction.csv │ │ │ │ │ ├── gtf │ │ │ │ │ │ ├── gencode.vM10.annotation.subset.gtf │ │ │ │ │ │ ├── gencode.vM10.annotation.subset.gtf.db │ │ │ │ │ │ └── novel_exons.gtf │ │ │ │ │ ├── mxe │ │ │ │ │ │ ├── event.bed │ │ │ │ │ │ ├── events.csv │ │ │ │ │ │ ├── exon1.bed │ │ │ │ │ │ ├── exon2.bed │ │ │ │ │ │ ├── exon3.bed │ │ │ │ │ │ ├── exon4.bed │ │ │ │ │ │ ├── intron.bed │ │ │ │ │ │ ├── splice_sites.csv │ │ │ │ │ │ └── validated │ │ │ │ │ │ │ └── events.csv │ │ │ │ │ └── se │ │ │ │ │ │ ├── event.bed │ │ │ │ │ │ ├── events.csv │ │ │ │ │ │ ├── exon1.bed │ │ │ │ │ │ ├── exon2.bed │ │ │ │ │ │ ├── exon3.bed │ │ │ │ │ │ ├── intron.bed │ │ │ │ │ │ ├── splice_sites.csv │ │ │ │ │ │ └── validated │ │ │ │ │ │ └── events.csv │ │ │ │ ├── junctions │ │ │ │ │ ├── metadata.csv │ │ │ │ │ └── reads.csv │ │ │ │ └── psi │ │ │ │ │ ├── mxe │ │ │ │ │ ├── psi.csv │ │ │ │ │ └── summary.csv │ │ │ │ │ ├── outrigger_psi.csv │ │ │ │ │ ├── outrigger_summary.csv │ │ │ │ │ └── se │ │ │ │ │ ├── psi.csv │ │ │ │ │ └── summary.csv │ │ │ ├── outrigger_output_bam │ │ │ │ ├── index │ │ │ │ │ ├── exon_direction_junction.csv │ │ │ │ │ ├── gtf │ │ │ │ │ │ ├── gencode.vM10.annotation.subset.gtf │ │ │ │ │ │ ├── gencode.vM10.annotation.subset.gtf.db │ │ │ │ │ │ └── novel_exons.gtf │ │ │ │ │ ├── mxe │ │ │ │ │ │ ├── event.bed │ │ │ │ │ │ ├── events.csv │ │ │ │ │ │ ├── exon1.bed │ │ │ │ │ │ ├── exon2.bed │ │ │ │ │ │ ├── exon3.bed │ │ │ │ │ │ ├── exon4.bed │ │ │ │ │ │ └── intron.bed │ │ │ │ │ └── se │ │ │ │ │ │ ├── event.bed │ │ │ │ │ │ ├── events.csv │ │ │ │ │ │ ├── exon1.bed │ │ │ │ │ │ ├── exon2.bed │ │ │ │ │ │ ├── exon3.bed │ │ │ │ │ │ └── intron.bed │ │ │ │ ├── junctions │ │ │ │ │ ├── metadata.csv │ │ │ │ │ └── reads.csv │ │ │ │ └── psi │ │ │ │ │ ├── mxe │ │ │ │ │ ├── psi.csv │ │ │ │ │ └── summary.csv │ │ │ │ │ ├── outrigger_psi.csv │ │ │ │ │ ├── outrigger_summary.csv │ │ │ │ │ └── se │ │ │ │ │ ├── psi.csv │ │ │ │ │ └── summary.csv │ │ │ └── unprocessed │ │ │ │ ├── CAV_LP_Ipsi_tdTpos_cell_igv_load.txt │ │ │ │ ├── CAV_LP_Ipsi_tdTpos_cell_igv_session.xml │ │ │ │ ├── bam │ │ │ │ ├── CAV_LP_Ipsi_tdTpos_cell_1-SRR2140356-GSM1840944_R1.polyATrim.adapterTrim.rmRep.sorted.rg.subset.sorted.bam │ │ │ │ ├── CAV_LP_Ipsi_tdTpos_cell_1-SRR2140356-GSM1840944_R1.polyATrim.adapterTrim.rmRep.sorted.rg.subset.sorted.bam.bai │ │ │ │ ├── CAV_LP_Ipsi_tdTpos_cell_2-SRR2140357-GSM1840945_R1.polyATrim.adapterTrim.rmRep.sorted.rg.subset.sorted.bam │ │ │ │ └── CAV_LP_Ipsi_tdTpos_cell_2-SRR2140357-GSM1840945_R1.polyATrim.adapterTrim.rmRep.sorted.rg.subset.sorted.bam.bai │ │ │ │ ├── gtf │ │ │ │ ├── gencode.vM10.annotation.snap25.myl6.gtf │ │ │ │ ├── gencode.vM10.annotation.snap25.myl6.gtf.db │ │ │ │ ├── gencode.vM10.annotation.snap25.myl6.gtf.db.bak │ │ │ │ ├── gencode.vM10.annotation.subset.gtf │ │ │ │ ├── gencode.vM10.annotation.subset.gtf.db │ │ │ │ ├── gencode.vM10.annotation.subset.with.novel.gtf │ │ │ │ └── gencode.vM10.annotation.subset.with.novel.gtf.db │ │ │ │ ├── samtools_filter_subset.sh │ │ │ │ └── sj_out_tab │ │ │ │ ├── CAV_LP_Ipsi_tdTpos_cell_1-SRR2140356-GSM1840944_R1.polyATrim.adapterTrim.rmRep.bamSJ.out.tab │ │ │ │ ├── CAV_LP_Ipsi_tdTpos_cell_10-SRR2140365-GSM1840953_R1.polyATrim.adapterTrim.rmRep.bamSJ.out.tab │ │ │ │ ├── CAV_LP_Ipsi_tdTpos_cell_11-SRR2140366-GSM1840954_R1.polyATrim.adapterTrim.rmRep.bamSJ.out.tab │ │ │ │ ├── CAV_LP_Ipsi_tdTpos_cell_12-SRR2140367-GSM1840955_R1.polyATrim.adapterTrim.rmRep.bamSJ.out.tab │ │ │ │ ├── CAV_LP_Ipsi_tdTpos_cell_13-SRR2140368-GSM1840956_R1.polyATrim.adapterTrim.rmRep.bamSJ.out.tab │ │ │ │ ├── CAV_LP_Ipsi_tdTpos_cell_14-SRR2140369-GSM1840957_R1.polyATrim.adapterTrim.rmRep.bamSJ.out.tab │ │ │ │ ├── CAV_LP_Ipsi_tdTpos_cell_15-SRR2140370-GSM1840958_R1.polyATrim.adapterTrim.rmRep.bamSJ.out.tab │ │ │ │ ├── CAV_LP_Ipsi_tdTpos_cell_16-SRR2140371-GSM1840959_R1.polyATrim.adapterTrim.rmRep.bamSJ.out.tab │ │ │ │ ├── CAV_LP_Ipsi_tdTpos_cell_17-SRR2140372-GSM1840960_R1.polyATrim.adapterTrim.rmRep.bamSJ.out.tab │ │ │ │ ├── CAV_LP_Ipsi_tdTpos_cell_18-SRR2140373-GSM1840961_R1.polyATrim.adapterTrim.rmRep.bamSJ.out.tab │ │ │ │ ├── CAV_LP_Ipsi_tdTpos_cell_19-SRR2140374-GSM1840962_R1.polyATrim.adapterTrim.rmRep.bamSJ.out.tab │ │ │ │ ├── CAV_LP_Ipsi_tdTpos_cell_2-SRR2140357-GSM1840945_R1.polyATrim.adapterTrim.rmRep.bamSJ.out.tab │ │ │ │ ├── CAV_LP_Ipsi_tdTpos_cell_20-SRR2140375-GSM1840963_R1.polyATrim.adapterTrim.rmRep.bamSJ.out.tab │ │ │ │ ├── CAV_LP_Ipsi_tdTpos_cell_21-SRR2140376-GSM1840964_R1.polyATrim.adapterTrim.rmRep.bamSJ.out.tab │ │ │ │ ├── CAV_LP_Ipsi_tdTpos_cell_22-SRR2140377-GSM1840965_R1.polyATrim.adapterTrim.rmRep.bamSJ.out.tab │ │ │ │ ├── CAV_LP_Ipsi_tdTpos_cell_23-SRR2140378-GSM1840966_R1.polyATrim.adapterTrim.rmRep.bamSJ.out.tab │ │ │ │ ├── CAV_LP_Ipsi_tdTpos_cell_24-SRR2140379-GSM1840967_R1.polyATrim.adapterTrim.rmRep.bamSJ.out.tab │ │ │ │ ├── CAV_LP_Ipsi_tdTpos_cell_25-SRR2140380-GSM1840968_R1.polyATrim.adapterTrim.rmRep.bamSJ.out.tab │ │ │ │ ├── CAV_LP_Ipsi_tdTpos_cell_26-SRR2140381-GSM1840969_R1.polyATrim.adapterTrim.rmRep.bamSJ.out.tab │ │ │ │ ├── CAV_LP_Ipsi_tdTpos_cell_27-SRR2140382-GSM1840970_R1.polyATrim.adapterTrim.rmRep.bamSJ.out.tab │ │ │ │ ├── CAV_LP_Ipsi_tdTpos_cell_28-SRR2140383-GSM1840971_R1.polyATrim.adapterTrim.rmRep.bamSJ.out.tab │ │ │ │ ├── CAV_LP_Ipsi_tdTpos_cell_29-SRR2140384-GSM1840972_R1.polyATrim.adapterTrim.rmRep.bamSJ.out.tab │ │ │ │ ├── CAV_LP_Ipsi_tdTpos_cell_3-SRR2140358-GSM1840946_R1.polyATrim.adapterTrim.rmRep.bamSJ.out.tab │ │ │ │ ├── CAV_LP_Ipsi_tdTpos_cell_30-SRR2140385-GSM1840973_R1.polyATrim.adapterTrim.rmRep.bamSJ.out.tab │ │ │ │ ├── CAV_LP_Ipsi_tdTpos_cell_31-SRR2140386-GSM1840974_R1.polyATrim.adapterTrim.rmRep.bamSJ.out.tab │ │ │ │ ├── CAV_LP_Ipsi_tdTpos_cell_32-SRR2140387-GSM1840975_R1.polyATrim.adapterTrim.rmRep.bamSJ.out.tab │ │ │ │ ├── CAV_LP_Ipsi_tdTpos_cell_33-SRR2140388-GSM1840976_R1.polyATrim.adapterTrim.rmRep.bamSJ.out.tab │ │ │ │ ├── CAV_LP_Ipsi_tdTpos_cell_34-SRR2140389-GSM1840977_R1.polyATrim.adapterTrim.rmRep.bamSJ.out.tab │ │ │ │ ├── CAV_LP_Ipsi_tdTpos_cell_35-SRR2140390-GSM1840978_R1.polyATrim.adapterTrim.rmRep.bamSJ.out.tab │ │ │ │ ├── CAV_LP_Ipsi_tdTpos_cell_36-SRR2140391-GSM1840979_R1.polyATrim.adapterTrim.rmRep.bamSJ.out.tab │ │ │ │ ├── CAV_LP_Ipsi_tdTpos_cell_37-SRR2140392-GSM1840980_R1.polyATrim.adapterTrim.rmRep.bamSJ.out.tab │ │ │ │ ├── CAV_LP_Ipsi_tdTpos_cell_38-SRR2140393-GSM1840981_R1.polyATrim.adapterTrim.rmRep.bamSJ.out.tab │ │ │ │ ├── CAV_LP_Ipsi_tdTpos_cell_39-SRR2140394-GSM1840982_R1.polyATrim.adapterTrim.rmRep.bamSJ.out.tab │ │ │ │ ├── CAV_LP_Ipsi_tdTpos_cell_4-SRR2140359-GSM1840947_R1.polyATrim.adapterTrim.rmRep.bamSJ.out.tab │ │ │ │ ├── CAV_LP_Ipsi_tdTpos_cell_40-SRR2140395-GSM1840983_R1.polyATrim.adapterTrim.rmRep.bamSJ.out.tab │ │ │ │ ├── CAV_LP_Ipsi_tdTpos_cell_41-SRR2140396-GSM1840984_R1.polyATrim.adapterTrim.rmRep.bamSJ.out.tab │ │ │ │ ├── CAV_LP_Ipsi_tdTpos_cell_42-SRR2140397-GSM1840985_R1.polyATrim.adapterTrim.rmRep.bamSJ.out.tab │ │ │ │ ├── CAV_LP_Ipsi_tdTpos_cell_43-SRR2140398-GSM1840986_R1.polyATrim.adapterTrim.rmRep.bamSJ.out.tab │ │ │ │ ├── CAV_LP_Ipsi_tdTpos_cell_5-SRR2140360-GSM1840948_R1.polyATrim.adapterTrim.rmRep.bamSJ.out.tab │ │ │ │ ├── CAV_LP_Ipsi_tdTpos_cell_6-SRR2140361-GSM1840949_R1.polyATrim.adapterTrim.rmRep.bamSJ.out.tab │ │ │ │ ├── CAV_LP_Ipsi_tdTpos_cell_7-SRR2140362-GSM1840950_R1.polyATrim.adapterTrim.rmRep.bamSJ.out.tab │ │ │ │ ├── CAV_LP_Ipsi_tdTpos_cell_8-SRR2140363-GSM1840951_R1.polyATrim.adapterTrim.rmRep.bamSJ.out.tab │ │ │ │ ├── CAV_LP_Ipsi_tdTpos_cell_9-SRR2140364-GSM1840952_R1.polyATrim.adapterTrim.rmRep.bamSJ.out.tab │ │ │ │ ├── Rbp4_CTX_10pg_1-SRR2140404-GSM1840992_R1.polyATrim.adapterTrim.rmRep.bamSJ.out.tab │ │ │ │ ├── Rbp4_CTX_10pg_2-SRR2140405-GSM1840993_R1.polyATrim.adapterTrim.rmRep.bamSJ.out.tab │ │ │ │ ├── Rbp4_CTX_10pg_3-SRR2140406-GSM1840994_R1.polyATrim.adapterTrim.rmRep.bamSJ.out.tab │ │ │ │ ├── Rbp4_CTX_10pg_4-SRR2140407-GSM1840995_R1.polyATrim.adapterTrim.rmRep.bamSJ.out.tab │ │ │ │ ├── Rbp4_CTX_10pg_5-SRR2140408-GSM1840996_R1.polyATrim.adapterTrim.rmRep.bamSJ.out.tab │ │ │ │ ├── Rbp4_CTX_10pg_6-SRR2140409-GSM1840997_R1.polyATrim.adapterTrim.rmRep.bamSJ.out.tab │ │ │ │ ├── Rbp4_CTX_250ng_1-SRR2140410-GSM1840998_R1.polyATrim.adapterTrim.rmRep.bamSJ.out.tab │ │ │ │ ├── Rbp4_CTX_250ng_2-SRR2140411-GSM1840999_R1.polyATrim.adapterTrim.rmRep.bamSJ.out.tab │ │ │ │ ├── Rbp4_tdTnegative_cell_1-SRR2139859-GSM1840447_R1.polyATrim.adapterTrim.rmRep.bamSJ.out.tab │ │ │ │ ├── Rbp4_tdTnegative_cell_10-SRR2139868-GSM1840456_R1.polyATrim.adapterTrim.rmRep.bamSJ.out.tab │ │ │ │ ├── Rbp4_tdTnegative_cell_11-SRR2139869-GSM1840457_R1.polyATrim.adapterTrim.rmRep.bamSJ.out.tab │ │ │ │ ├── Rbp4_tdTnegative_cell_12-SRR2139870-GSM1840458_R1.polyATrim.adapterTrim.rmRep.bamSJ.out.tab │ │ │ │ ├── Rbp4_tdTnegative_cell_13-SRR2139871-GSM1840459_R1.polyATrim.adapterTrim.rmRep.bamSJ.out.tab │ │ │ │ ├── Rbp4_tdTnegative_cell_14-SRR2139872-GSM1840460_R1.polyATrim.adapterTrim.rmRep.bamSJ.out.tab │ │ │ │ ├── Rbp4_tdTnegative_cell_15-SRR2139873-GSM1840461_R1.polyATrim.adapterTrim.rmRep.bamSJ.out.tab │ │ │ │ ├── Rbp4_tdTnegative_cell_16-SRR2139874-GSM1840462_R1.polyATrim.adapterTrim.rmRep.bamSJ.out.tab │ │ │ │ ├── Rbp4_tdTnegative_cell_17-SRR2139875-GSM1840463_R1.polyATrim.adapterTrim.rmRep.bamSJ.out.tab │ │ │ │ ├── Rbp4_tdTnegative_cell_18-SRR2139876-GSM1840464_R1.polyATrim.adapterTrim.rmRep.bamSJ.out.tab │ │ │ │ ├── Rbp4_tdTnegative_cell_19-SRR2139877-GSM1840465_R1.polyATrim.adapterTrim.rmRep.bamSJ.out.tab │ │ │ │ ├── Rbp4_tdTnegative_cell_2-SRR2139860-GSM1840448_R1.polyATrim.adapterTrim.rmRep.bamSJ.out.tab │ │ │ │ ├── Rbp4_tdTnegative_cell_20-SRR2139878-GSM1840466_R1.polyATrim.adapterTrim.rmRep.bamSJ.out.tab │ │ │ │ ├── Rbp4_tdTnegative_cell_21-SRR2139879-GSM1840467_R1.polyATrim.adapterTrim.rmRep.bamSJ.out.tab │ │ │ │ ├── Rbp4_tdTnegative_cell_22-SRR2139880-GSM1840468_R1.polyATrim.adapterTrim.rmRep.bamSJ.out.tab │ │ │ │ ├── Rbp4_tdTnegative_cell_23-SRR2139881-GSM1840469_R1.polyATrim.adapterTrim.rmRep.bamSJ.out.tab │ │ │ │ ├── Rbp4_tdTnegative_cell_3-SRR2139861-GSM1840449_R1.polyATrim.adapterTrim.rmRep.bamSJ.out.tab │ │ │ │ ├── Rbp4_tdTnegative_cell_4-SRR2139862-GSM1840450_R1.polyATrim.adapterTrim.rmRep.bamSJ.out.tab │ │ │ │ ├── Rbp4_tdTnegative_cell_5-SRR2139863-GSM1840451_R1.polyATrim.adapterTrim.rmRep.bamSJ.out.tab │ │ │ │ ├── Rbp4_tdTnegative_cell_6-SRR2139864-GSM1840452_R1.polyATrim.adapterTrim.rmRep.bamSJ.out.tab │ │ │ │ ├── Rbp4_tdTnegative_cell_7-SRR2139865-GSM1840453_R1.polyATrim.adapterTrim.rmRep.bamSJ.out.tab │ │ │ │ ├── Rbp4_tdTnegative_cell_8-SRR2139866-GSM1840454_R1.polyATrim.adapterTrim.rmRep.bamSJ.out.tab │ │ │ │ ├── Rbp4_tdTnegative_cell_9-SRR2139867-GSM1840455_R1.polyATrim.adapterTrim.rmRep.bamSJ.out.tab │ │ │ │ ├── Rbp4_tdTpositive_cell_1-SRR2139669-GSM1840257_R1.polyATrim.adapterTrim.rmRep.bamSJ.out.tab │ │ │ │ ├── Rbp4_tdTpositive_cell_10-SRR2139678-GSM1840266_R1.polyATrim.adapterTrim.rmRep.bamSJ.out.tab │ │ │ │ ├── Rbp4_tdTpositive_cell_100-SRR2139768-GSM1840356_R1.polyATrim.adapterTrim.rmRep.bamSJ.out.tab │ │ │ │ ├── Rbp4_tdTpositive_cell_101-SRR2139769-GSM1840357_R1.polyATrim.adapterTrim.rmRep.bamSJ.out.tab │ │ │ │ ├── Rbp4_tdTpositive_cell_102-SRR2139770-GSM1840358_R1.polyATrim.adapterTrim.rmRep.bamSJ.out.tab │ │ │ │ ├── Rbp4_tdTpositive_cell_103-SRR2139771-GSM1840359_R1.polyATrim.adapterTrim.rmRep.bamSJ.out.tab │ │ │ │ ├── Rbp4_tdTpositive_cell_104-SRR2139772-GSM1840360_R1.polyATrim.adapterTrim.rmRep.bamSJ.out.tab │ │ │ │ ├── Rbp4_tdTpositive_cell_105-SRR2139773-GSM1840361_R1.polyATrim.adapterTrim.rmRep.bamSJ.out.tab │ │ │ │ ├── Rbp4_tdTpositive_cell_106-SRR2139774-GSM1840362_R1.polyATrim.adapterTrim.rmRep.bamSJ.out.tab │ │ │ │ ├── Rbp4_tdTpositive_cell_107-SRR2139775-GSM1840363_R1.polyATrim.adapterTrim.rmRep.bamSJ.out.tab │ │ │ │ ├── Rbp4_tdTpositive_cell_108-SRR2139776-GSM1840364_R1.polyATrim.adapterTrim.rmRep.bamSJ.out.tab │ │ │ │ ├── Rbp4_tdTpositive_cell_109-SRR2139777-GSM1840365_R1.polyATrim.adapterTrim.rmRep.bamSJ.out.tab │ │ │ │ ├── Rbp4_tdTpositive_cell_11-SRR2139679-GSM1840267_R1.polyATrim.adapterTrim.rmRep.bamSJ.out.tab │ │ │ │ ├── Rbp4_tdTpositive_cell_110-SRR2139778-GSM1840366_R1.polyATrim.adapterTrim.rmRep.bamSJ.out.tab │ │ │ │ ├── Rbp4_tdTpositive_cell_111-SRR2139779-GSM1840367_R1.polyATrim.adapterTrim.rmRep.bamSJ.out.tab │ │ │ │ ├── Rbp4_tdTpositive_cell_112-SRR2139780-GSM1840368_R1.polyATrim.adapterTrim.rmRep.bamSJ.out.tab │ │ │ │ ├── Rbp4_tdTpositive_cell_113-SRR2139781-GSM1840369_R1.polyATrim.adapterTrim.rmRep.bamSJ.out.tab │ │ │ │ ├── Rbp4_tdTpositive_cell_114-SRR2139782-GSM1840370_R1.polyATrim.adapterTrim.rmRep.bamSJ.out.tab │ │ │ │ ├── Rbp4_tdTpositive_cell_115-SRR2139783-GSM1840371_R1.polyATrim.adapterTrim.rmRep.bamSJ.out.tab │ │ │ │ ├── Rbp4_tdTpositive_cell_116-SRR2139784-GSM1840372_R1.polyATrim.adapterTrim.rmRep.bamSJ.out.tab │ │ │ │ ├── Rbp4_tdTpositive_cell_117-SRR2139785-GSM1840373_R1.polyATrim.adapterTrim.rmRep.bamSJ.out.tab │ │ │ │ ├── Rbp4_tdTpositive_cell_118-SRR2139786-GSM1840374_R1.polyATrim.adapterTrim.rmRep.bamSJ.out.tab │ │ │ │ ├── Rbp4_tdTpositive_cell_119-SRR2139787-GSM1840375_R1.polyATrim.adapterTrim.rmRep.bamSJ.out.tab │ │ │ │ ├── Rbp4_tdTpositive_cell_12-SRR2139680-GSM1840268_R1.polyATrim.adapterTrim.rmRep.bamSJ.out.tab │ │ │ │ ├── Rbp4_tdTpositive_cell_120-SRR2139788-GSM1840376_R1.polyATrim.adapterTrim.rmRep.bamSJ.out.tab │ │ │ │ ├── Rbp4_tdTpositive_cell_121-SRR2139789-GSM1840377_R1.polyATrim.adapterTrim.rmRep.bamSJ.out.tab │ │ │ │ ├── Rbp4_tdTpositive_cell_122-SRR2139790-GSM1840378_R1.polyATrim.adapterTrim.rmRep.bamSJ.out.tab │ │ │ │ ├── Rbp4_tdTpositive_cell_123-SRR2139791-GSM1840379_R1.polyATrim.adapterTrim.rmRep.bamSJ.out.tab │ │ │ │ ├── Rbp4_tdTpositive_cell_124-SRR2139792-GSM1840380_R1.polyATrim.adapterTrim.rmRep.bamSJ.out.tab │ │ │ │ ├── Rbp4_tdTpositive_cell_125-SRR2139793-GSM1840381_R1.polyATrim.adapterTrim.rmRep.bamSJ.out.tab │ │ │ │ ├── Rbp4_tdTpositive_cell_126-SRR2139794-GSM1840382_R1.polyATrim.adapterTrim.rmRep.bamSJ.out.tab │ │ │ │ ├── Rbp4_tdTpositive_cell_127-SRR2139795-GSM1840383_R1.polyATrim.adapterTrim.rmRep.bamSJ.out.tab │ │ │ │ ├── Rbp4_tdTpositive_cell_128-SRR2139796-GSM1840384_R1.polyATrim.adapterTrim.rmRep.bamSJ.out.tab │ │ │ │ ├── Rbp4_tdTpositive_cell_129-SRR2139797-GSM1840385_R1.polyATrim.adapterTrim.rmRep.bamSJ.out.tab │ │ │ │ ├── Rbp4_tdTpositive_cell_13-SRR2139681-GSM1840269_R1.polyATrim.adapterTrim.rmRep.bamSJ.out.tab │ │ │ │ ├── Rbp4_tdTpositive_cell_130-SRR2139798-GSM1840386_R1.polyATrim.adapterTrim.rmRep.bamSJ.out.tab │ │ │ │ ├── Rbp4_tdTpositive_cell_131-SRR2139799-GSM1840387_R1.polyATrim.adapterTrim.rmRep.bamSJ.out.tab │ │ │ │ ├── Rbp4_tdTpositive_cell_132-SRR2139800-GSM1840388_R1.polyATrim.adapterTrim.rmRep.bamSJ.out.tab │ │ │ │ ├── Rbp4_tdTpositive_cell_133-SRR2139801-GSM1840389_R1.polyATrim.adapterTrim.rmRep.bamSJ.out.tab │ │ │ │ ├── Rbp4_tdTpositive_cell_134-SRR2139802-GSM1840390_R1.polyATrim.adapterTrim.rmRep.bamSJ.out.tab │ │ │ │ ├── Rbp4_tdTpositive_cell_135-SRR2139803-GSM1840391_R1.polyATrim.adapterTrim.rmRep.bamSJ.out.tab │ │ │ │ ├── Rbp4_tdTpositive_cell_136-SRR2139804-GSM1840392_R1.polyATrim.adapterTrim.rmRep.bamSJ.out.tab │ │ │ │ ├── Rbp4_tdTpositive_cell_137-SRR2139805-GSM1840393_R1.polyATrim.adapterTrim.rmRep.bamSJ.out.tab │ │ │ │ ├── Rbp4_tdTpositive_cell_138-SRR2139806-GSM1840394_R1.polyATrim.adapterTrim.rmRep.bamSJ.out.tab │ │ │ │ ├── Rbp4_tdTpositive_cell_139-SRR2139807-GSM1840395_R1.polyATrim.adapterTrim.rmRep.bamSJ.out.tab │ │ │ │ ├── Rbp4_tdTpositive_cell_14-SRR2139682-GSM1840270_R1.polyATrim.adapterTrim.rmRep.bamSJ.out.tab │ │ │ │ ├── Rbp4_tdTpositive_cell_140-SRR2139808-GSM1840396_R1.polyATrim.adapterTrim.rmRep.bamSJ.out.tab │ │ │ │ ├── Rbp4_tdTpositive_cell_141-SRR2139809-GSM1840397_R1.polyATrim.adapterTrim.rmRep.bamSJ.out.tab │ │ │ │ ├── Rbp4_tdTpositive_cell_142-SRR2139810-GSM1840398_R1.polyATrim.adapterTrim.rmRep.bamSJ.out.tab │ │ │ │ ├── Rbp4_tdTpositive_cell_143-SRR2139811-GSM1840399_R1.polyATrim.adapterTrim.rmRep.bamSJ.out.tab │ │ │ │ ├── Rbp4_tdTpositive_cell_144-SRR2139812-GSM1840400_R1.polyATrim.adapterTrim.rmRep.bamSJ.out.tab │ │ │ │ ├── Rbp4_tdTpositive_cell_145-SRR2139813-GSM1840401_R1.polyATrim.adapterTrim.rmRep.bamSJ.out.tab │ │ │ │ ├── Rbp4_tdTpositive_cell_146-SRR2139814-GSM1840402_R1.polyATrim.adapterTrim.rmRep.bamSJ.out.tab │ │ │ │ ├── Rbp4_tdTpositive_cell_147-SRR2139815-GSM1840403_R1.polyATrim.adapterTrim.rmRep.bamSJ.out.tab │ │ │ │ ├── Rbp4_tdTpositive_cell_148-SRR2139816-GSM1840404_R1.polyATrim.adapterTrim.rmRep.bamSJ.out.tab │ │ │ │ ├── Rbp4_tdTpositive_cell_149-SRR2139817-GSM1840405_R1.polyATrim.adapterTrim.rmRep.bamSJ.out.tab │ │ │ │ ├── Rbp4_tdTpositive_cell_15-SRR2139683-GSM1840271_R1.polyATrim.adapterTrim.rmRep.bamSJ.out.tab │ │ │ │ ├── Rbp4_tdTpositive_cell_150-SRR2139818-GSM1840406_R1.polyATrim.adapterTrim.rmRep.bamSJ.out.tab │ │ │ │ ├── Rbp4_tdTpositive_cell_151-SRR2139819-GSM1840407_R1.polyATrim.adapterTrim.rmRep.bamSJ.out.tab │ │ │ │ ├── Rbp4_tdTpositive_cell_152-SRR2139820-GSM1840408_R1.polyATrim.adapterTrim.rmRep.bamSJ.out.tab │ │ │ │ ├── Rbp4_tdTpositive_cell_153-SRR2139821-GSM1840409_R1.polyATrim.adapterTrim.rmRep.bamSJ.out.tab │ │ │ │ ├── Rbp4_tdTpositive_cell_154-SRR2139822-GSM1840410_R1.polyATrim.adapterTrim.rmRep.bamSJ.out.tab │ │ │ │ ├── Rbp4_tdTpositive_cell_155-SRR2139823-GSM1840411_R1.polyATrim.adapterTrim.rmRep.bamSJ.out.tab │ │ │ │ ├── Rbp4_tdTpositive_cell_156-SRR2139824-GSM1840412_R1.polyATrim.adapterTrim.rmRep.bamSJ.out.tab │ │ │ │ ├── Rbp4_tdTpositive_cell_157-SRR2139825-GSM1840413_R1.polyATrim.adapterTrim.rmRep.bamSJ.out.tab │ │ │ │ ├── Rbp4_tdTpositive_cell_158-SRR2139826-GSM1840414_R1.polyATrim.adapterTrim.rmRep.bamSJ.out.tab │ │ │ │ ├── Rbp4_tdTpositive_cell_159-SRR2139827-GSM1840415_R1.polyATrim.adapterTrim.rmRep.bamSJ.out.tab │ │ │ │ ├── Rbp4_tdTpositive_cell_16-SRR2139684-GSM1840272_R1.polyATrim.adapterTrim.rmRep.bamSJ.out.tab │ │ │ │ ├── Rbp4_tdTpositive_cell_160-SRR2139828-GSM1840416_R1.polyATrim.adapterTrim.rmRep.bamSJ.out.tab │ │ │ │ ├── Rbp4_tdTpositive_cell_161-SRR2139829-GSM1840417_R1.polyATrim.adapterTrim.rmRep.bamSJ.out.tab │ │ │ │ ├── Rbp4_tdTpositive_cell_162-SRR2139830-GSM1840418_R1.polyATrim.adapterTrim.rmRep.bamSJ.out.tab │ │ │ │ ├── Rbp4_tdTpositive_cell_163-SRR2139831-GSM1840419_R1.polyATrim.adapterTrim.rmRep.bamSJ.out.tab │ │ │ │ ├── Rbp4_tdTpositive_cell_164-SRR2139832-GSM1840420_R1.polyATrim.adapterTrim.rmRep.bamSJ.out.tab │ │ │ │ ├── Rbp4_tdTpositive_cell_165-SRR2139833-GSM1840421_R1.polyATrim.adapterTrim.rmRep.bamSJ.out.tab │ │ │ │ ├── Rbp4_tdTpositive_cell_166-SRR2139834-GSM1840422_R1.polyATrim.adapterTrim.rmRep.bamSJ.out.tab │ │ │ │ ├── Rbp4_tdTpositive_cell_167-SRR2139835-GSM1840423_R1.polyATrim.adapterTrim.rmRep.bamSJ.out.tab │ │ │ │ ├── Rbp4_tdTpositive_cell_168-SRR2139836-GSM1840424_R1.polyATrim.adapterTrim.rmRep.bamSJ.out.tab │ │ │ │ ├── Rbp4_tdTpositive_cell_169-SRR2139837-GSM1840425_R1.polyATrim.adapterTrim.rmRep.bamSJ.out.tab │ │ │ │ ├── Rbp4_tdTpositive_cell_17-SRR2139685-GSM1840273_R1.polyATrim.adapterTrim.rmRep.bamSJ.out.tab │ │ │ │ ├── Rbp4_tdTpositive_cell_170-SRR2139838-GSM1840426_R1.polyATrim.adapterTrim.rmRep.bamSJ.out.tab │ │ │ │ ├── Rbp4_tdTpositive_cell_171-SRR2139839-GSM1840427_R1.polyATrim.adapterTrim.rmRep.bamSJ.out.tab │ │ │ │ ├── Rbp4_tdTpositive_cell_172-SRR2139840-GSM1840428_R1.polyATrim.adapterTrim.rmRep.bamSJ.out.tab │ │ │ │ ├── Rbp4_tdTpositive_cell_173-SRR2139841-GSM1840429_R1.polyATrim.adapterTrim.rmRep.bamSJ.out.tab │ │ │ │ ├── Rbp4_tdTpositive_cell_174-SRR2139842-GSM1840430_R1.polyATrim.adapterTrim.rmRep.bamSJ.out.tab │ │ │ │ ├── Rbp4_tdTpositive_cell_175-SRR2139843-GSM1840431_R1.polyATrim.adapterTrim.rmRep.bamSJ.out.tab │ │ │ │ ├── Rbp4_tdTpositive_cell_176-SRR2139844-GSM1840432_R1.polyATrim.adapterTrim.rmRep.bamSJ.out.tab │ │ │ │ ├── Rbp4_tdTpositive_cell_177-SRR2139845-GSM1840433_R1.polyATrim.adapterTrim.rmRep.bamSJ.out.tab │ │ │ │ ├── Rbp4_tdTpositive_cell_178-SRR2139846-GSM1840434_R1.polyATrim.adapterTrim.rmRep.bamSJ.out.tab │ │ │ │ ├── Rbp4_tdTpositive_cell_179-SRR2139847-GSM1840435_R1.polyATrim.adapterTrim.rmRep.bamSJ.out.tab │ │ │ │ ├── Rbp4_tdTpositive_cell_18-SRR2139686-GSM1840274_R1.polyATrim.adapterTrim.rmRep.bamSJ.out.tab │ │ │ │ ├── Rbp4_tdTpositive_cell_180-SRR2139848-GSM1840436_R1.polyATrim.adapterTrim.rmRep.bamSJ.out.tab │ │ │ │ ├── Rbp4_tdTpositive_cell_181-SRR2139849-GSM1840437_R1.polyATrim.adapterTrim.rmRep.bamSJ.out.tab │ │ │ │ ├── Rbp4_tdTpositive_cell_182-SRR2139850-GSM1840438_R1.polyATrim.adapterTrim.rmRep.bamSJ.out.tab │ │ │ │ ├── Rbp4_tdTpositive_cell_183-SRR2139851-GSM1840439_R1.polyATrim.adapterTrim.rmRep.bamSJ.out.tab │ │ │ │ ├── Rbp4_tdTpositive_cell_184-SRR2139852-GSM1840440_R1.polyATrim.adapterTrim.rmRep.bamSJ.out.tab │ │ │ │ ├── Rbp4_tdTpositive_cell_185-SRR2139853-GSM1840441_R1.polyATrim.adapterTrim.rmRep.bamSJ.out.tab │ │ │ │ ├── Rbp4_tdTpositive_cell_186-SRR2139854-GSM1840442_R1.polyATrim.adapterTrim.rmRep.bamSJ.out.tab │ │ │ │ ├── Rbp4_tdTpositive_cell_187-SRR2139855-GSM1840443_R1.polyATrim.adapterTrim.rmRep.bamSJ.out.tab │ │ │ │ ├── Rbp4_tdTpositive_cell_188-SRR2139856-GSM1840444_R1.polyATrim.adapterTrim.rmRep.bamSJ.out.tab │ │ │ │ ├── Rbp4_tdTpositive_cell_189-SRR2139857-GSM1840445_R1.polyATrim.adapterTrim.rmRep.bamSJ.out.tab │ │ │ │ ├── Rbp4_tdTpositive_cell_19-SRR2139687-GSM1840275_R1.polyATrim.adapterTrim.rmRep.bamSJ.out.tab │ │ │ │ ├── Rbp4_tdTpositive_cell_190-SRR2139858-GSM1840446_R1.polyATrim.adapterTrim.rmRep.bamSJ.out.tab │ │ │ │ ├── Rbp4_tdTpositive_cell_2-SRR2139670-GSM1840258_R1.polyATrim.adapterTrim.rmRep.bamSJ.out.tab │ │ │ │ ├── Rbp4_tdTpositive_cell_20-SRR2139688-GSM1840276_R1.polyATrim.adapterTrim.rmRep.bamSJ.out.tab │ │ │ │ ├── Rbp4_tdTpositive_cell_21-SRR2139689-GSM1840277_R1.polyATrim.adapterTrim.rmRep.bamSJ.out.tab │ │ │ │ ├── Rbp4_tdTpositive_cell_22-SRR2139690-GSM1840278_R1.polyATrim.adapterTrim.rmRep.bamSJ.out.tab │ │ │ │ ├── Rbp4_tdTpositive_cell_23-SRR2139691-GSM1840279_R1.polyATrim.adapterTrim.rmRep.bamSJ.out.tab │ │ │ │ ├── Rbp4_tdTpositive_cell_24-SRR2139692-GSM1840280_R1.polyATrim.adapterTrim.rmRep.bamSJ.out.tab │ │ │ │ ├── Rbp4_tdTpositive_cell_25-SRR2139693-GSM1840281_R1.polyATrim.adapterTrim.rmRep.bamSJ.out.tab │ │ │ │ ├── Rbp4_tdTpositive_cell_26-SRR2139694-GSM1840282_R1.polyATrim.adapterTrim.rmRep.bamSJ.out.tab │ │ │ │ ├── Rbp4_tdTpositive_cell_27-SRR2139695-GSM1840283_R1.polyATrim.adapterTrim.rmRep.bamSJ.out.tab │ │ │ │ ├── Rbp4_tdTpositive_cell_28-SRR2139696-GSM1840284_R1.polyATrim.adapterTrim.rmRep.bamSJ.out.tab │ │ │ │ ├── Rbp4_tdTpositive_cell_29-SRR2139697-GSM1840285_R1.polyATrim.adapterTrim.rmRep.bamSJ.out.tab │ │ │ │ ├── Rbp4_tdTpositive_cell_3-SRR2139671-GSM1840259_R1.polyATrim.adapterTrim.rmRep.bamSJ.out.tab │ │ │ │ ├── Rbp4_tdTpositive_cell_30-SRR2139698-GSM1840286_R1.polyATrim.adapterTrim.rmRep.bamSJ.out.tab │ │ │ │ ├── Rbp4_tdTpositive_cell_31-SRR2139699-GSM1840287_R1.polyATrim.adapterTrim.rmRep.bamSJ.out.tab │ │ │ │ ├── Rbp4_tdTpositive_cell_32-SRR2139700-GSM1840288_R1.polyATrim.adapterTrim.rmRep.bamSJ.out.tab │ │ │ │ ├── Rbp4_tdTpositive_cell_33-SRR2139701-GSM1840289_R1.polyATrim.adapterTrim.rmRep.bamSJ.out.tab │ │ │ │ ├── Rbp4_tdTpositive_cell_34-SRR2139702-GSM1840290_R1.polyATrim.adapterTrim.rmRep.bamSJ.out.tab │ │ │ │ ├── Rbp4_tdTpositive_cell_35-SRR2139703-GSM1840291_R1.polyATrim.adapterTrim.rmRep.bamSJ.out.tab │ │ │ │ ├── Rbp4_tdTpositive_cell_36-SRR2139704-GSM1840292_R1.polyATrim.adapterTrim.rmRep.bamSJ.out.tab │ │ │ │ ├── Rbp4_tdTpositive_cell_37-SRR2139705-GSM1840293_R1.polyATrim.adapterTrim.rmRep.bamSJ.out.tab │ │ │ │ ├── Rbp4_tdTpositive_cell_38-SRR2139706-GSM1840294_R1.polyATrim.adapterTrim.rmRep.bamSJ.out.tab │ │ │ │ ├── Rbp4_tdTpositive_cell_39-SRR2139707-GSM1840295_R1.polyATrim.adapterTrim.rmRep.bamSJ.out.tab │ │ │ │ ├── Rbp4_tdTpositive_cell_4-SRR2139672-GSM1840260_R1.polyATrim.adapterTrim.rmRep.bamSJ.out.tab │ │ │ │ ├── Rbp4_tdTpositive_cell_40-SRR2139708-GSM1840296_R1.polyATrim.adapterTrim.rmRep.bamSJ.out.tab │ │ │ │ ├── Rbp4_tdTpositive_cell_41-SRR2139709-GSM1840297_R1.polyATrim.adapterTrim.rmRep.bamSJ.out.tab │ │ │ │ ├── Rbp4_tdTpositive_cell_42-SRR2139710-GSM1840298_R1.polyATrim.adapterTrim.rmRep.bamSJ.out.tab │ │ │ │ ├── Rbp4_tdTpositive_cell_43-SRR2139711-GSM1840299_R1.polyATrim.adapterTrim.rmRep.bamSJ.out.tab │ │ │ │ ├── Rbp4_tdTpositive_cell_44-SRR2139712-GSM1840300_R1.polyATrim.adapterTrim.rmRep.bamSJ.out.tab │ │ │ │ ├── Rbp4_tdTpositive_cell_45-SRR2139713-GSM1840301_R1.polyATrim.adapterTrim.rmRep.bamSJ.out.tab │ │ │ │ ├── Rbp4_tdTpositive_cell_46-SRR2139714-GSM1840302_R1.polyATrim.adapterTrim.rmRep.bamSJ.out.tab │ │ │ │ ├── Rbp4_tdTpositive_cell_47-SRR2139715-GSM1840303_R1.polyATrim.adapterTrim.rmRep.bamSJ.out.tab │ │ │ │ ├── Rbp4_tdTpositive_cell_48-SRR2139716-GSM1840304_R1.polyATrim.adapterTrim.rmRep.bamSJ.out.tab │ │ │ │ ├── Rbp4_tdTpositive_cell_49-SRR2139717-GSM1840305_R1.polyATrim.adapterTrim.rmRep.bamSJ.out.tab │ │ │ │ ├── Rbp4_tdTpositive_cell_5-SRR2139673-GSM1840261_R1.polyATrim.adapterTrim.rmRep.bamSJ.out.tab │ │ │ │ ├── Rbp4_tdTpositive_cell_50-SRR2139718-GSM1840306_R1.polyATrim.adapterTrim.rmRep.bamSJ.out.tab │ │ │ │ ├── Rbp4_tdTpositive_cell_51-SRR2139719-GSM1840307_R1.polyATrim.adapterTrim.rmRep.bamSJ.out.tab │ │ │ │ ├── Rbp4_tdTpositive_cell_52-SRR2139720-GSM1840308_R1.polyATrim.adapterTrim.rmRep.bamSJ.out.tab │ │ │ │ ├── Rbp4_tdTpositive_cell_53-SRR2139721-GSM1840309_R1.polyATrim.adapterTrim.rmRep.bamSJ.out.tab │ │ │ │ ├── Rbp4_tdTpositive_cell_54-SRR2139722-GSM1840310_R1.polyATrim.adapterTrim.rmRep.bamSJ.out.tab │ │ │ │ ├── Rbp4_tdTpositive_cell_55-SRR2139723-GSM1840311_R1.polyATrim.adapterTrim.rmRep.bamSJ.out.tab │ │ │ │ ├── Rbp4_tdTpositive_cell_56-SRR2139724-GSM1840312_R1.polyATrim.adapterTrim.rmRep.bamSJ.out.tab │ │ │ │ ├── Rbp4_tdTpositive_cell_57-SRR2139725-GSM1840313_R1.polyATrim.adapterTrim.rmRep.bamSJ.out.tab │ │ │ │ ├── Rbp4_tdTpositive_cell_58-SRR2139726-GSM1840314_R1.polyATrim.adapterTrim.rmRep.bamSJ.out.tab │ │ │ │ ├── Rbp4_tdTpositive_cell_59-SRR2139727-GSM1840315_R1.polyATrim.adapterTrim.rmRep.bamSJ.out.tab │ │ │ │ ├── Rbp4_tdTpositive_cell_6-SRR2139674-GSM1840262_R1.polyATrim.adapterTrim.rmRep.bamSJ.out.tab │ │ │ │ ├── Rbp4_tdTpositive_cell_60-SRR2139728-GSM1840316_R1.polyATrim.adapterTrim.rmRep.bamSJ.out.tab │ │ │ │ ├── Rbp4_tdTpositive_cell_61-SRR2139729-GSM1840317_R1.polyATrim.adapterTrim.rmRep.bamSJ.out.tab │ │ │ │ ├── Rbp4_tdTpositive_cell_62-SRR2139730-GSM1840318_R1.polyATrim.adapterTrim.rmRep.bamSJ.out.tab │ │ │ │ ├── Rbp4_tdTpositive_cell_63-SRR2139731-GSM1840319_R1.polyATrim.adapterTrim.rmRep.bamSJ.out.tab │ │ │ │ ├── Rbp4_tdTpositive_cell_64-SRR2139732-GSM1840320_R1.polyATrim.adapterTrim.rmRep.bamSJ.out.tab │ │ │ │ ├── Rbp4_tdTpositive_cell_65-SRR2139733-GSM1840321_R1.polyATrim.adapterTrim.rmRep.bamSJ.out.tab │ │ │ │ ├── Rbp4_tdTpositive_cell_66-SRR2139734-GSM1840322_R1.polyATrim.adapterTrim.rmRep.bamSJ.out.tab │ │ │ │ ├── Rbp4_tdTpositive_cell_67-SRR2139735-GSM1840323_R1.polyATrim.adapterTrim.rmRep.bamSJ.out.tab │ │ │ │ ├── Rbp4_tdTpositive_cell_68-SRR2139736-GSM1840324_R1.polyATrim.adapterTrim.rmRep.bamSJ.out.tab │ │ │ │ ├── Rbp4_tdTpositive_cell_69-SRR2139737-GSM1840325_R1.polyATrim.adapterTrim.rmRep.bamSJ.out.tab │ │ │ │ ├── Rbp4_tdTpositive_cell_7-SRR2139675-GSM1840263_R1.polyATrim.adapterTrim.rmRep.bamSJ.out.tab │ │ │ │ ├── Rbp4_tdTpositive_cell_70-SRR2139738-GSM1840326_R1.polyATrim.adapterTrim.rmRep.bamSJ.out.tab │ │ │ │ ├── Rbp4_tdTpositive_cell_71-SRR2139739-GSM1840327_R1.polyATrim.adapterTrim.rmRep.bamSJ.out.tab │ │ │ │ ├── Rbp4_tdTpositive_cell_72-SRR2139740-GSM1840328_R1.polyATrim.adapterTrim.rmRep.bamSJ.out.tab │ │ │ │ ├── Rbp4_tdTpositive_cell_73-SRR2139741-GSM1840329_R1.polyATrim.adapterTrim.rmRep.bamSJ.out.tab │ │ │ │ ├── Rbp4_tdTpositive_cell_74-SRR2139742-GSM1840330_R1.polyATrim.adapterTrim.rmRep.bamSJ.out.tab │ │ │ │ ├── Rbp4_tdTpositive_cell_75-SRR2139743-GSM1840331_R1.polyATrim.adapterTrim.rmRep.bamSJ.out.tab │ │ │ │ ├── Rbp4_tdTpositive_cell_76-SRR2139744-GSM1840332_R1.polyATrim.adapterTrim.rmRep.bamSJ.out.tab │ │ │ │ ├── Rbp4_tdTpositive_cell_77-SRR2139745-GSM1840333_R1.polyATrim.adapterTrim.rmRep.bamSJ.out.tab │ │ │ │ ├── Rbp4_tdTpositive_cell_78-SRR2139746-GSM1840334_R1.polyATrim.adapterTrim.rmRep.bamSJ.out.tab │ │ │ │ ├── Rbp4_tdTpositive_cell_79-SRR2139747-GSM1840335_R1.polyATrim.adapterTrim.rmRep.bamSJ.out.tab │ │ │ │ ├── Rbp4_tdTpositive_cell_8-SRR2139676-GSM1840264_R1.polyATrim.adapterTrim.rmRep.bamSJ.out.tab │ │ │ │ ├── Rbp4_tdTpositive_cell_80-SRR2139748-GSM1840336_R1.polyATrim.adapterTrim.rmRep.bamSJ.out.tab │ │ │ │ ├── Rbp4_tdTpositive_cell_81-SRR2139749-GSM1840337_R1.polyATrim.adapterTrim.rmRep.bamSJ.out.tab │ │ │ │ ├── Rbp4_tdTpositive_cell_82-SRR2139750-GSM1840338_R1.polyATrim.adapterTrim.rmRep.bamSJ.out.tab │ │ │ │ ├── Rbp4_tdTpositive_cell_83-SRR2139751-GSM1840339_R1.polyATrim.adapterTrim.rmRep.bamSJ.out.tab │ │ │ │ ├── Rbp4_tdTpositive_cell_84-SRR2139752-GSM1840340_R1.polyATrim.adapterTrim.rmRep.bamSJ.out.tab │ │ │ │ ├── Rbp4_tdTpositive_cell_85-SRR2139753-GSM1840341_R1.polyATrim.adapterTrim.rmRep.bamSJ.out.tab │ │ │ │ ├── Rbp4_tdTpositive_cell_86-SRR2139754-GSM1840342_R1.polyATrim.adapterTrim.rmRep.bamSJ.out.tab │ │ │ │ ├── Rbp4_tdTpositive_cell_87-SRR2139755-GSM1840343_R1.polyATrim.adapterTrim.rmRep.bamSJ.out.tab │ │ │ │ ├── Rbp4_tdTpositive_cell_88-SRR2139756-GSM1840344_R1.polyATrim.adapterTrim.rmRep.bamSJ.out.tab │ │ │ │ ├── Rbp4_tdTpositive_cell_89-SRR2139757-GSM1840345_R1.polyATrim.adapterTrim.rmRep.bamSJ.out.tab │ │ │ │ ├── Rbp4_tdTpositive_cell_9-SRR2139677-GSM1840265_R1.polyATrim.adapterTrim.rmRep.bamSJ.out.tab │ │ │ │ ├── Rbp4_tdTpositive_cell_90-SRR2139758-GSM1840346_R1.polyATrim.adapterTrim.rmRep.bamSJ.out.tab │ │ │ │ ├── Rbp4_tdTpositive_cell_91-SRR2139759-GSM1840347_R1.polyATrim.adapterTrim.rmRep.bamSJ.out.tab │ │ │ │ ├── Rbp4_tdTpositive_cell_92-SRR2139760-GSM1840348_R1.polyATrim.adapterTrim.rmRep.bamSJ.out.tab │ │ │ │ ├── Rbp4_tdTpositive_cell_93-SRR2139761-GSM1840349_R1.polyATrim.adapterTrim.rmRep.bamSJ.out.tab │ │ │ │ ├── Rbp4_tdTpositive_cell_94-SRR2139762-GSM1840350_R1.polyATrim.adapterTrim.rmRep.bamSJ.out.tab │ │ │ │ ├── Rbp4_tdTpositive_cell_95-SRR2139763-GSM1840351_R1.polyATrim.adapterTrim.rmRep.bamSJ.out.tab │ │ │ │ ├── Rbp4_tdTpositive_cell_96-SRR2139764-GSM1840352_R1.polyATrim.adapterTrim.rmRep.bamSJ.out.tab │ │ │ │ ├── Rbp4_tdTpositive_cell_97-SRR2139765-GSM1840353_R1.polyATrim.adapterTrim.rmRep.bamSJ.out.tab │ │ │ │ ├── Rbp4_tdTpositive_cell_98-SRR2139766-GSM1840354_R1.polyATrim.adapterTrim.rmRep.bamSJ.out.tab │ │ │ │ └── Rbp4_tdTpositive_cell_99-SRR2139767-GSM1840355_R1.polyATrim.adapterTrim.rmRep.bamSJ.out.tab │ │ └── treutlein2014 │ │ │ ├── intermediate │ │ │ ├── index │ │ │ │ └── adjacencies │ │ │ │ │ ├── adjacent_junctions_single_exon.csv │ │ │ │ │ ├── junctions_genome_adjacent_to_exon_downstream.csv │ │ │ │ │ ├── junctions_genome_adjacent_to_exon_upstream.csv │ │ │ │ │ ├── neighboring_exons.csv │ │ │ │ │ └── single_junction_exon_triple.csv │ │ │ └── io │ │ │ │ └── star │ │ │ │ ├── junction_metadata.csv │ │ │ │ ├── splice_junctions_multimappingFalse.csv │ │ │ │ └── splice_junctions_multimappingTrue.csv │ │ │ └── unprocessed │ │ │ ├── gtf │ │ │ ├── gencode.vM2.annotation.fgfr2.gtf │ │ │ └── gencode.vM2.annotation.fgfr2.gtf.db │ │ │ └── sj_out_tab │ │ │ ├── SRR1033853_1.polyATrim.adapterTrim.rmRep.bamSJ.out.tab │ │ │ ├── SRR1033854_1.polyATrim.adapterTrim.rmRep.bamSJ.out.tab │ │ │ ├── SRR1033855_1.polyATrim.adapterTrim.rmRep.bamSJ.out.tab │ │ │ ├── SRR1033856_1.polyATrim.adapterTrim.rmRep.bamSJ.out.tab │ │ │ ├── SRR1033857_1.polyATrim.adapterTrim.rmRep.bamSJ.out.tab │ │ │ ├── SRR1033858_1.polyATrim.adapterTrim.rmRep.bamSJ.out.tab │ │ │ ├── SRR1033859_1.polyATrim.adapterTrim.rmRep.bamSJ.out.tab │ │ │ ├── SRR1033860_1.polyATrim.adapterTrim.rmRep.bamSJ.out.tab │ │ │ ├── SRR1033861_1.polyATrim.adapterTrim.rmRep.bamSJ.out.tab │ │ │ ├── SRR1033862_1.polyATrim.adapterTrim.rmRep.bamSJ.out.tab │ │ │ ├── SRR1033863_1.polyATrim.adapterTrim.rmRep.bamSJ.out.tab │ │ │ ├── SRR1033864_1.polyATrim.adapterTrim.rmRep.bamSJ.out.tab │ │ │ ├── SRR1033865_1.polyATrim.adapterTrim.rmRep.bamSJ.out.tab │ │ │ ├── SRR1033866_1.polyATrim.adapterTrim.rmRep.bamSJ.out.tab │ │ │ ├── SRR1033867_1.polyATrim.adapterTrim.rmRep.bamSJ.out.tab │ │ │ ├── SRR1033868_1.polyATrim.adapterTrim.rmRep.bamSJ.out.tab │ │ │ ├── SRR1033869_1.polyATrim.adapterTrim.rmRep.bamSJ.out.tab │ │ │ ├── SRR1033870_1.polyATrim.adapterTrim.rmRep.bamSJ.out.tab │ │ │ ├── SRR1033871_1.polyATrim.adapterTrim.rmRep.bamSJ.out.tab │ │ │ ├── SRR1033872_1.polyATrim.adapterTrim.rmRep.bamSJ.out.tab │ │ │ ├── SRR1033873_1.polyATrim.adapterTrim.rmRep.bamSJ.out.tab │ │ │ ├── SRR1033874_1.polyATrim.adapterTrim.rmRep.bamSJ.out.tab │ │ │ ├── SRR1033875_1.polyATrim.adapterTrim.rmRep.bamSJ.out.tab │ │ │ ├── SRR1033876_1.polyATrim.adapterTrim.rmRep.bamSJ.out.tab │ │ │ ├── SRR1033877_1.polyATrim.adapterTrim.rmRep.bamSJ.out.tab │ │ │ ├── SRR1033878_1.polyATrim.adapterTrim.rmRep.bamSJ.out.tab │ │ │ ├── SRR1033879_1.polyATrim.adapterTrim.rmRep.bamSJ.out.tab │ │ │ ├── SRR1033880_1.polyATrim.adapterTrim.rmRep.bamSJ.out.tab │ │ │ ├── SRR1033881_1.polyATrim.adapterTrim.rmRep.bamSJ.out.tab │ │ │ ├── SRR1033882_1.polyATrim.adapterTrim.rmRep.bamSJ.out.tab │ │ │ ├── SRR1033883_1.polyATrim.adapterTrim.rmRep.bamSJ.out.tab │ │ │ ├── SRR1033884_1.polyATrim.adapterTrim.rmRep.bamSJ.out.tab │ │ │ ├── SRR1033885_1.polyATrim.adapterTrim.rmRep.bamSJ.out.tab │ │ │ ├── SRR1033886_1.polyATrim.adapterTrim.rmRep.bamSJ.out.tab │ │ │ ├── SRR1033887_1.polyATrim.adapterTrim.rmRep.bamSJ.out.tab │ │ │ ├── SRR1033888_1.polyATrim.adapterTrim.rmRep.bamSJ.out.tab │ │ │ ├── SRR1033889_1.polyATrim.adapterTrim.rmRep.bamSJ.out.tab │ │ │ ├── SRR1033890_1.polyATrim.adapterTrim.rmRep.bamSJ.out.tab │ │ │ ├── SRR1033891_1.polyATrim.adapterTrim.rmRep.bamSJ.out.tab │ │ │ ├── SRR1033892_1.polyATrim.adapterTrim.rmRep.bamSJ.out.tab │ │ │ ├── SRR1033893_1.polyATrim.adapterTrim.rmRep.bamSJ.out.tab │ │ │ ├── SRR1033894_1.polyATrim.adapterTrim.rmRep.bamSJ.out.tab │ │ │ ├── SRR1033895_1.polyATrim.adapterTrim.rmRep.bamSJ.out.tab │ │ │ ├── SRR1033896_1.polyATrim.adapterTrim.rmRep.bamSJ.out.tab │ │ │ ├── SRR1033897_1.polyATrim.adapterTrim.rmRep.bamSJ.out.tab │ │ │ ├── SRR1033898_1.polyATrim.adapterTrim.rmRep.bamSJ.out.tab │ │ │ ├── SRR1033899_1.polyATrim.adapterTrim.rmRep.bamSJ.out.tab │ │ │ ├── SRR1033900_1.polyATrim.adapterTrim.rmRep.bamSJ.out.tab │ │ │ ├── SRR1033901_1.polyATrim.adapterTrim.rmRep.bamSJ.out.tab │ │ │ ├── SRR1033902_1.polyATrim.adapterTrim.rmRep.bamSJ.out.tab │ │ │ ├── SRR1033903_1.polyATrim.adapterTrim.rmRep.bamSJ.out.tab │ │ │ ├── SRR1033904_1.polyATrim.adapterTrim.rmRep.bamSJ.out.tab │ │ │ ├── SRR1033905_1.polyATrim.adapterTrim.rmRep.bamSJ.out.tab │ │ │ ├── SRR1033906_1.polyATrim.adapterTrim.rmRep.bamSJ.out.tab │ │ │ ├── SRR1033907_1.polyATrim.adapterTrim.rmRep.bamSJ.out.tab │ │ │ ├── SRR1033908_1.polyATrim.adapterTrim.rmRep.bamSJ.out.tab │ │ │ ├── SRR1033909_1.polyATrim.adapterTrim.rmRep.bamSJ.out.tab │ │ │ ├── SRR1033910_1.polyATrim.adapterTrim.rmRep.bamSJ.out.tab │ │ │ ├── SRR1033911_1.polyATrim.adapterTrim.rmRep.bamSJ.out.tab │ │ │ ├── SRR1033912_1.polyATrim.adapterTrim.rmRep.bamSJ.out.tab │ │ │ ├── SRR1033913_1.polyATrim.adapterTrim.rmRep.bamSJ.out.tab │ │ │ ├── SRR1033914_1.polyATrim.adapterTrim.rmRep.bamSJ.out.tab │ │ │ ├── SRR1033915_1.polyATrim.adapterTrim.rmRep.bamSJ.out.tab │ │ │ ├── SRR1033916_1.polyATrim.adapterTrim.rmRep.bamSJ.out.tab │ │ │ ├── SRR1033917_1.polyATrim.adapterTrim.rmRep.bamSJ.out.tab │ │ │ ├── SRR1033918_1.polyATrim.adapterTrim.rmRep.bamSJ.out.tab │ │ │ ├── SRR1033919_1.polyATrim.adapterTrim.rmRep.bamSJ.out.tab │ │ │ ├── SRR1033920_1.polyATrim.adapterTrim.rmRep.bamSJ.out.tab │ │ │ ├── SRR1033921_1.polyATrim.adapterTrim.rmRep.bamSJ.out.tab │ │ │ ├── SRR1033922_1.polyATrim.adapterTrim.rmRep.bamSJ.out.tab │ │ │ ├── SRR1033923_1.polyATrim.adapterTrim.rmRep.bamSJ.out.tab │ │ │ ├── SRR1033924_1.polyATrim.adapterTrim.rmRep.bamSJ.out.tab │ │ │ ├── SRR1033925_1.polyATrim.adapterTrim.rmRep.bamSJ.out.tab │ │ │ ├── SRR1033926_1.polyATrim.adapterTrim.rmRep.bamSJ.out.tab │ │ │ ├── SRR1033927_1.polyATrim.adapterTrim.rmRep.bamSJ.out.tab │ │ │ ├── SRR1033928_1.polyATrim.adapterTrim.rmRep.bamSJ.out.tab │ │ │ ├── SRR1033929_1.polyATrim.adapterTrim.rmRep.bamSJ.out.tab │ │ │ ├── SRR1033930_1.polyATrim.adapterTrim.rmRep.bamSJ.out.tab │ │ │ ├── SRR1033931_1.polyATrim.adapterTrim.rmRep.bamSJ.out.tab │ │ │ ├── SRR1033932_1.polyATrim.adapterTrim.rmRep.bamSJ.out.tab │ │ │ ├── SRR1033933_1.polyATrim.adapterTrim.rmRep.bamSJ.out.tab │ │ │ ├── SRR1033934_1.polyATrim.adapterTrim.rmRep.bamSJ.out.tab │ │ │ ├── SRR1033935_1.polyATrim.adapterTrim.rmRep.bamSJ.out.tab │ │ │ ├── SRR1033936_1.polyATrim.adapterTrim.rmRep.bamSJ.out.tab │ │ │ ├── SRR1033937_1.polyATrim.adapterTrim.rmRep.bamSJ.out.tab │ │ │ ├── SRR1033938_1.polyATrim.adapterTrim.rmRep.bamSJ.out.tab │ │ │ ├── SRR1033939_1.polyATrim.adapterTrim.rmRep.bamSJ.out.tab │ │ │ ├── SRR1033940_1.polyATrim.adapterTrim.rmRep.bamSJ.out.tab │ │ │ ├── SRR1033941_1.polyATrim.adapterTrim.rmRep.bamSJ.out.tab │ │ │ ├── SRR1033942_1.polyATrim.adapterTrim.rmRep.bamSJ.out.tab │ │ │ ├── SRR1033943_1.polyATrim.adapterTrim.rmRep.bamSJ.out.tab │ │ │ ├── SRR1033944_1.polyATrim.adapterTrim.rmRep.bamSJ.out.tab │ │ │ ├── SRR1033945_1.polyATrim.adapterTrim.rmRep.bamSJ.out.tab │ │ │ ├── SRR1033946_1.polyATrim.adapterTrim.rmRep.bamSJ.out.tab │ │ │ ├── SRR1033947_1.polyATrim.adapterTrim.rmRep.bamSJ.out.tab │ │ │ ├── SRR1033948_1.polyATrim.adapterTrim.rmRep.bamSJ.out.tab │ │ │ ├── SRR1033949_1.polyATrim.adapterTrim.rmRep.bamSJ.out.tab │ │ │ ├── SRR1033950_1.polyATrim.adapterTrim.rmRep.bamSJ.out.tab │ │ │ ├── SRR1033951_1.polyATrim.adapterTrim.rmRep.bamSJ.out.tab │ │ │ ├── SRR1033952_1.polyATrim.adapterTrim.rmRep.bamSJ.out.tab │ │ │ ├── SRR1033953_1.polyATrim.adapterTrim.rmRep.bamSJ.out.tab │ │ │ ├── SRR1033954_1.polyATrim.adapterTrim.rmRep.bamSJ.out.tab │ │ │ ├── SRR1033955_1.polyATrim.adapterTrim.rmRep.bamSJ.out.tab │ │ │ ├── SRR1033956_1.polyATrim.adapterTrim.rmRep.bamSJ.out.tab │ │ │ ├── SRR1033957_1.polyATrim.adapterTrim.rmRep.bamSJ.out.tab │ │ │ ├── SRR1033958_1.polyATrim.adapterTrim.rmRep.bamSJ.out.tab │ │ │ ├── SRR1033959_1.polyATrim.adapterTrim.rmRep.bamSJ.out.tab │ │ │ ├── SRR1033960_1.polyATrim.adapterTrim.rmRep.bamSJ.out.tab │ │ │ ├── SRR1033961_1.polyATrim.adapterTrim.rmRep.bamSJ.out.tab │ │ │ ├── SRR1033962_1.polyATrim.adapterTrim.rmRep.bamSJ.out.tab │ │ │ ├── SRR1033963_1.polyATrim.adapterTrim.rmRep.bamSJ.out.tab │ │ │ ├── SRR1033964_1.polyATrim.adapterTrim.rmRep.bamSJ.out.tab │ │ │ ├── SRR1033965_1.polyATrim.adapterTrim.rmRep.bamSJ.out.tab │ │ │ ├── SRR1033966_1.polyATrim.adapterTrim.rmRep.bamSJ.out.tab │ │ │ ├── SRR1033967_1.polyATrim.adapterTrim.rmRep.bamSJ.out.tab │ │ │ ├── SRR1033968_1.polyATrim.adapterTrim.rmRep.bamSJ.out.tab │ │ │ ├── SRR1033969_1.polyATrim.adapterTrim.rmRep.bamSJ.out.tab │ │ │ ├── SRR1033970_1.polyATrim.adapterTrim.rmRep.bamSJ.out.tab │ │ │ ├── SRR1033971_1.polyATrim.adapterTrim.rmRep.bamSJ.out.tab │ │ │ ├── SRR1033972_1.polyATrim.adapterTrim.rmRep.bamSJ.out.tab │ │ │ ├── SRR1033973_1.polyATrim.adapterTrim.rmRep.bamSJ.out.tab │ │ │ ├── SRR1033974_1.polyATrim.adapterTrim.rmRep.bamSJ.out.tab │ │ │ ├── SRR1033975_1.polyATrim.adapterTrim.rmRep.bamSJ.out.tab │ │ │ ├── SRR1033976_1.polyATrim.adapterTrim.rmRep.bamSJ.out.tab │ │ │ ├── SRR1033977_1.polyATrim.adapterTrim.rmRep.bamSJ.out.tab │ │ │ ├── SRR1033978_1.polyATrim.adapterTrim.rmRep.bamSJ.out.tab │ │ │ ├── SRR1033979_1.polyATrim.adapterTrim.rmRep.bamSJ.out.tab │ │ │ ├── SRR1033980_1.polyATrim.adapterTrim.rmRep.bamSJ.out.tab │ │ │ ├── SRR1033981_1.polyATrim.adapterTrim.rmRep.bamSJ.out.tab │ │ │ ├── SRR1033982_1.polyATrim.adapterTrim.rmRep.bamSJ.out.tab │ │ │ ├── SRR1033983_1.polyATrim.adapterTrim.rmRep.bamSJ.out.tab │ │ │ ├── SRR1033984_1.polyATrim.adapterTrim.rmRep.bamSJ.out.tab │ │ │ ├── SRR1033985_1.polyATrim.adapterTrim.rmRep.bamSJ.out.tab │ │ │ ├── SRR1033986_1.polyATrim.adapterTrim.rmRep.bamSJ.out.tab │ │ │ ├── SRR1033987_1.polyATrim.adapterTrim.rmRep.bamSJ.out.tab │ │ │ ├── SRR1033988_1.polyATrim.adapterTrim.rmRep.bamSJ.out.tab │ │ │ ├── SRR1033989_1.polyATrim.adapterTrim.rmRep.bamSJ.out.tab │ │ │ ├── SRR1033990_1.polyATrim.adapterTrim.rmRep.bamSJ.out.tab │ │ │ ├── SRR1033991_1.polyATrim.adapterTrim.rmRep.bamSJ.out.tab │ │ │ ├── SRR1033992_1.polyATrim.adapterTrim.rmRep.bamSJ.out.tab │ │ │ ├── SRR1033993_1.polyATrim.adapterTrim.rmRep.bamSJ.out.tab │ │ │ ├── SRR1033994_1.polyATrim.adapterTrim.rmRep.bamSJ.out.tab │ │ │ ├── SRR1033995_1.polyATrim.adapterTrim.rmRep.bamSJ.out.tab │ │ │ ├── SRR1033996_1.polyATrim.adapterTrim.rmRep.bamSJ.out.tab │ │ │ ├── SRR1033997_1.polyATrim.adapterTrim.rmRep.bamSJ.out.tab │ │ │ ├── SRR1033998_1.polyATrim.adapterTrim.rmRep.bamSJ.out.tab │ │ │ ├── SRR1033999_1.polyATrim.adapterTrim.rmRep.bamSJ.out.tab │ │ │ ├── SRR1034000_1.polyATrim.adapterTrim.rmRep.bamSJ.out.tab │ │ │ ├── SRR1034001_1.polyATrim.adapterTrim.rmRep.bamSJ.out.tab │ │ │ ├── SRR1034002_1.polyATrim.adapterTrim.rmRep.bamSJ.out.tab │ │ │ ├── SRR1034003_1.polyATrim.adapterTrim.rmRep.bamSJ.out.tab │ │ │ ├── SRR1034004_1.polyATrim.adapterTrim.rmRep.bamSJ.out.tab │ │ │ ├── SRR1034005_1.polyATrim.adapterTrim.rmRep.bamSJ.out.tab │ │ │ ├── SRR1034006_1.polyATrim.adapterTrim.rmRep.bamSJ.out.tab │ │ │ ├── SRR1034007_1.polyATrim.adapterTrim.rmRep.bamSJ.out.tab │ │ │ ├── SRR1034008_1.polyATrim.adapterTrim.rmRep.bamSJ.out.tab │ │ │ ├── SRR1034009_1.polyATrim.adapterTrim.rmRep.bamSJ.out.tab │ │ │ ├── SRR1034010_1.polyATrim.adapterTrim.rmRep.bamSJ.out.tab │ │ │ ├── SRR1034011_1.polyATrim.adapterTrim.rmRep.bamSJ.out.tab │ │ │ ├── SRR1034012_1.polyATrim.adapterTrim.rmRep.bamSJ.out.tab │ │ │ ├── SRR1034013_1.polyATrim.adapterTrim.rmRep.bamSJ.out.tab │ │ │ ├── SRR1034014_1.polyATrim.adapterTrim.rmRep.bamSJ.out.tab │ │ │ ├── SRR1034015_1.polyATrim.adapterTrim.rmRep.bamSJ.out.tab │ │ │ ├── SRR1034016_1.polyATrim.adapterTrim.rmRep.bamSJ.out.tab │ │ │ ├── SRR1034017_1.polyATrim.adapterTrim.rmRep.bamSJ.out.tab │ │ │ ├── SRR1034018_1.polyATrim.adapterTrim.rmRep.bamSJ.out.tab │ │ │ ├── SRR1034019_1.polyATrim.adapterTrim.rmRep.bamSJ.out.tab │ │ │ ├── SRR1034020_1.polyATrim.adapterTrim.rmRep.bamSJ.out.tab │ │ │ ├── SRR1034021_1.polyATrim.adapterTrim.rmRep.bamSJ.out.tab │ │ │ ├── SRR1034022_1.polyATrim.adapterTrim.rmRep.bamSJ.out.tab │ │ │ ├── SRR1034023_1.polyATrim.adapterTrim.rmRep.bamSJ.out.tab │ │ │ ├── SRR1034024_1.polyATrim.adapterTrim.rmRep.bamSJ.out.tab │ │ │ ├── SRR1034025_1.polyATrim.adapterTrim.rmRep.bamSJ.out.tab │ │ │ ├── SRR1034026_1.polyATrim.adapterTrim.rmRep.bamSJ.out.tab │ │ │ ├── SRR1034027_1.polyATrim.adapterTrim.rmRep.bamSJ.out.tab │ │ │ ├── SRR1034028_1.polyATrim.adapterTrim.rmRep.bamSJ.out.tab │ │ │ ├── SRR1034029_1.polyATrim.adapterTrim.rmRep.bamSJ.out.tab │ │ │ ├── SRR1034030_1.polyATrim.adapterTrim.rmRep.bamSJ.out.tab │ │ │ ├── SRR1034031_1.polyATrim.adapterTrim.rmRep.bamSJ.out.tab │ │ │ ├── SRR1034032_1.polyATrim.adapterTrim.rmRep.bamSJ.out.tab │ │ │ ├── SRR1034033_1.polyATrim.adapterTrim.rmRep.bamSJ.out.tab │ │ │ ├── SRR1034034_1.polyATrim.adapterTrim.rmRep.bamSJ.out.tab │ │ │ ├── SRR1034035_1.polyATrim.adapterTrim.rmRep.bamSJ.out.tab │ │ │ ├── SRR1034036_1.polyATrim.adapterTrim.rmRep.bamSJ.out.tab │ │ │ ├── SRR1034037_1.polyATrim.adapterTrim.rmRep.bamSJ.out.tab │ │ │ ├── SRR1034038_1.polyATrim.adapterTrim.rmRep.bamSJ.out.tab │ │ │ ├── SRR1034039_1.polyATrim.adapterTrim.rmRep.bamSJ.out.tab │ │ │ ├── SRR1034040_1.polyATrim.adapterTrim.rmRep.bamSJ.out.tab │ │ │ ├── SRR1034041_1.polyATrim.adapterTrim.rmRep.bamSJ.out.tab │ │ │ ├── SRR1034042_1.polyATrim.adapterTrim.rmRep.bamSJ.out.tab │ │ │ ├── SRR1034043_1.polyATrim.adapterTrim.rmRep.bamSJ.out.tab │ │ │ ├── SRR1034044_1.polyATrim.adapterTrim.rmRep.bamSJ.out.tab │ │ │ ├── SRR1034045_1.polyATrim.adapterTrim.rmRep.bamSJ.out.tab │ │ │ ├── SRR1034046_1.polyATrim.adapterTrim.rmRep.bamSJ.out.tab │ │ │ ├── SRR1034047_1.polyATrim.adapterTrim.rmRep.bamSJ.out.tab │ │ │ ├── SRR1034048_1.polyATrim.adapterTrim.rmRep.bamSJ.out.tab │ │ │ ├── SRR1034049_1.polyATrim.adapterTrim.rmRep.bamSJ.out.tab │ │ │ ├── SRR1034050_1.polyATrim.adapterTrim.rmRep.bamSJ.out.tab │ │ │ ├── SRR1034051_1.polyATrim.adapterTrim.rmRep.bamSJ.out.tab │ │ │ ├── SRR1034052_1.polyATrim.adapterTrim.rmRep.bamSJ.out.tab │ │ │ └── SRR1034053_1.polyATrim.adapterTrim.rmRep.bamSJ.out.tab │ ├── hmmscan_out.txt │ ├── index │ │ ├── __init__.py │ │ ├── test_adjacencies.py │ │ ├── test_events.py │ │ └── test_region.py │ ├── io │ │ ├── __init__.py │ │ ├── test_bam.py │ │ ├── test_gtf.py │ │ └── test_star.py │ ├── psi │ │ ├── __init__.py │ │ └── test_compute.py │ ├── test.bed │ ├── test.chromsizes │ ├── test.fasta │ ├── test.fasta.fai │ ├── test_commandline.py │ └── validate │ │ ├── __init__.py │ │ └── test_check_splice_sites.py ├── util.py └── validate │ ├── __init__.py │ └── check_splice_sites.py ├── requirements.txt ├── setup.cfg ├── setup.py └── testing └── environment_no_python.yml /.editorconfig: -------------------------------------------------------------------------------- 1 | # http://editorconfig.org 2 | 3 | root = true 4 | 5 | [*] 6 | indent_style = space 7 | indent_size = 4 8 | trim_trailing_whitespace = true 9 | insert_final_newline = true 10 | charset = utf-8 11 | end_of_line = lf 12 | 13 | [*.bat] 14 | indent_style = tab 15 | end_of_line = crlf 16 | 17 | [LICENSE] 18 | insert_final_newline = false 19 | 20 | [Makefile] 21 | indent_style = tab 22 | -------------------------------------------------------------------------------- /.github/ISSUE_TEMPLATE.md: -------------------------------------------------------------------------------- 1 | Hi! Thanks for using Outrigger. 2 | 3 | If you are reporting an issue or a feature request: 4 | 5 | - Please use the [GitHub issue](https://github.com/yeolab/outrigger/issues) 6 | search feature to check if your issue has been asked already. If it has, 7 | please add your comments to the existing issue. 8 | 9 | - Where applicable, please fill out the details below to help us troubleshoot 10 | the issue that you are facing. Please be as thorough as you are able to 11 | provide details on the issue. 12 | 13 | ### Description 14 | 15 | [Description of the bug or feature] 16 | 17 | ### Steps to Reproduce 18 | 19 | 1. [First Step] 20 | 2. [Second Step] 21 | 3. [and so on...] 22 | 23 | **Expected behavior:** [What you expected to happen] 24 | 25 | **Actual behavior:** [What actually happened] 26 | 27 | ### Versions 28 | 29 | You can get this information from executing `outrigger --version` at the 30 | command line. 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Why not be the first? 14 | -------------------------------------------------------------------------------- /LICENSE: -------------------------------------------------------------------------------- 1 | Copyright (c) 2015, Olga Botvinnik 2 | All rights reserved. 3 | 4 | Redistribution and use in source and binary forms, with or without modification, are permitted provided that the following conditions are met: 5 | 6 | * Redistributions of source code must retain the above copyright notice, this list of conditions and the following disclaimer. 7 | 8 | * Redistributions in binary form must reproduce the above copyright notice, this list of conditions and the following disclaimer in the documentation and/or other materials provided with the distribution. 9 | 10 | * Neither the name of BED annotator nor the names of its contributors may be used to endorse or promote products derived from this software without specific prior written permission. 11 | 12 | THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS" AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT HOLDER OR CONTRIBUTORS BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE. -------------------------------------------------------------------------------- /MANIFEST.in: -------------------------------------------------------------------------------- 1 | include AUTHORS.rst 2 | include CONTRIBUTING.rst 3 | include HISTORY.rst 4 | include LICENSE 5 | include README.rst 6 | include requirements.txt 7 | 8 | recursive-include tests * 9 | recursive-exclude * __pycache__ 10 | recursive-exclude * *.py[co] 11 | 12 | recursive-include docs *.rst conf.py Makefile make.bat 13 | -------------------------------------------------------------------------------- /codecov.yml: -------------------------------------------------------------------------------- 1 | codecov: 2 | token: 6e443b9c-c0b8-4683-8df7-85a961f9f8d9 3 | branch: master 4 | bot: null 5 | 6 | coverage: 7 | precision: 2 8 | round: down 9 | range: "70...100" 10 | 11 | notify: 12 | slack: 13 | default: 14 | url: null 15 | threshold: null 16 | branches: null 17 | attachments: "sunburst, diff" 18 | 19 | hipchat: 20 | default: 21 | url: null 22 | notify: no 23 | threshold: null 24 | branches: null 25 | card: yes 26 | only_pulls: null 27 | message: null 28 | 29 | gitter: 30 | default: 31 | url: null 32 | threshold: null 33 | branches: null 34 | message: null 35 | 36 | webhook: 37 | default: 38 | url: null 39 | threshold: null 40 | branches: null 41 | only_pulls: null 42 | 43 | irc: 44 | default: 45 | server: null 46 | channel: null 47 | branches: null 48 | threshold: null 49 | message: null 50 | 51 | status: 52 | project: 53 | default: 54 | target: auto 55 | threshold: null 56 | branches: null 57 | 58 | patch: 59 | default: 60 | target: auto 61 | branches: null 62 | 63 | changes: 64 | default: 65 | branches: null 66 | 67 | ignore: null 68 | 69 | comment: 70 | layout: "header, diff, changes, sunburst, uncovered, tree" 71 | branches: null 72 | behavior: default 73 | -------------------------------------------------------------------------------- /conda_requirements.txt: -------------------------------------------------------------------------------- 1 | pytest>=3.0.0 2 | pandas>=0.17.0 3 | coverage 4 | gffutils 5 | pybedtools 6 | biopython 7 | joblib 8 | pysam 9 | bedtools 10 | -------------------------------------------------------------------------------- /docs/CHANGELOG_sphinx_deployment.md: -------------------------------------------------------------------------------- 1 | Change Log 2 | ========== 3 | 4 | [0.3.0][] (2013-11-26) 5 | ---------------------- 6 | 7 | - Improvement 8 | + [SPXD-10] - Deploy vX.X.X tag to docs/X.X.X instead of docs/vX.X.X 9 | 10 | - New Feature 11 | + [SPXD-9] - PaaS deployment: heroku 12 | 13 | - Migration (from v0.2.0 to v0.3.0) 14 | + `REPO_URL` was changed to `REPO_URL_GITHUB` 15 | + `DEPLOY_BRANCH` was changed to `DEPLOY_BRANCH_GITHUB` 16 | + `$ make push` was changed to `$ make deploy_gh_pages` 17 | + `$ make rsync` was changed to `$ make deploy_rsync` 18 | 19 | 20 | [0.2.0][] (2013-09-26) 21 | ---------------------- 22 | 23 | - Improvement 24 | + [SPXD-6] - remove duplication of git init when setup_gh_pages 25 | 26 | - New Feature 27 | + [SPXD-5] - Rsync support 28 | 29 | 30 | [0.1.0][] (2013-08-18) 31 | ---------------------- 32 | 33 | - Improvement 34 | + [SPXD-2] - remove "make init_gh_pages" step 35 | 36 | - New Feature 37 | + [SPXD-1] - make gen_deploy 38 | + [SPXD-3] - installation bash script 39 | 40 | 41 | [0.1.0]: https://issues.teracy.org/secure/ReleaseNote.jspa?version=10003&styleName=Text&projectId=10405&Create=Create&atl_token=BD5N-YNBS-EHHQ-478Z%7C87dd31199258f9de5ade180582481463461ded32%7Clin 42 | 43 | [0.2.0]: https://issues.teracy.org/secure/ReleaseNote.jspa?projectId=10405&version=10004 44 | 45 | [0.3.0]: https://issues.teracy.org/secure/ReleaseNote.jspa?projectId=10405&version=10301 46 | -------------------------------------------------------------------------------- /docs/LICENSE_sphinx_deployment: -------------------------------------------------------------------------------- 1 | Copyright (c) Teracy, Inc. and individual contributors. 2 | All rights reserved. 3 | 4 | Redistribution and use in source and binary forms, with or without modification, 5 | are permitted provided that the following conditions are met: 6 | 7 | 1. Redistributions of source code must retain the above copyright notice, 8 | this list of conditions and the following disclaimer. 9 | 10 | 2. Redistributions in binary form must reproduce the above copyright 11 | notice, this list of conditions and the following disclaimer in the 12 | documentation and/or other materials provided with the distribution. 13 | 14 | 3. Neither the name of Teracy, Inc. nor the names of its contributors may be used 15 | to endorse or promote products derived from this software without 16 | specific prior written permission. 17 | 18 | THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS" AND 19 | ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE IMPLIED 20 | WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE 21 | DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT OWNER OR CONTRIBUTORS BE LIABLE FOR 22 | ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES 23 | (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; 24 | LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON 25 | ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT 26 | (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS 27 | SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE. 28 | -------------------------------------------------------------------------------- /docs/_static/exon_vs_junction_start_stop.ai: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/YeoLab/outrigger/9da86d2d8d137b309a53cae8851ba867cf757201/docs/_static/exon_vs_junction_start_stop.ai -------------------------------------------------------------------------------- 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-------------------------------------------------------------------------------- /docs/index.rst: -------------------------------------------------------------------------------- 1 | .. outrigger documentation master file, created by 2 | sphinx-quickstart on Tue Jul 9 22:26:36 2013. 3 | You can adapt this file completely to your liking, but it should at least 4 | contain the root `toctree` directive. 5 | 6 | Welcome to ``outrigger``'s documentation! 7 | ========================================= 8 | 9 | .. include:: ../README.rst 10 | 11 | 12 | Contents: 13 | 14 | .. toctree:: 15 | :maxdepth: 2 16 | 17 | installation 18 | usage 19 | contributing 20 | authors 21 | history 22 | 23 | Indices and tables 24 | ================== 25 | 26 | * :ref:`genindex` 27 | * :ref:`modindex` 28 | * :ref:`search` 29 | 30 | .. |OutriggerLogo| image:: https://raw.githubusercontent.com/YeoLab/outrigger/master/logo/logo_v1.png 31 | .. |BuildStatus| image:: https://travis-ci.org/YeoLab/outrigger.svg?branch=master 32 | :target: https://travis-ci.org/YeoLab/outrigger 33 | .. |codecov| image:: https://codecov.io/gh/YeoLab/outrigger/branch/master/graph/badge.svg 34 | :target: https://codecov.io/gh/YeoLab/outrigger 35 | .. |PyPI versions| image:: https://img.shields.io/pypi/v/outrigger.svg 36 | :target: https://pypi.python.org/pypi/outrigger 37 | .. |PythonVersionCompatibility| image:: https://img.shields.io/pypi/pyversions/outrigger.svg 38 | :target: https://pypi.python.org/pypi/outrigger 39 | .. |license| image:: https://img.shields.io/github/pypi/l/outrigger.svg 40 | :target: 41 | -------------------------------------------------------------------------------- /docs/installation.rst: -------------------------------------------------------------------------------- 1 | ============ 2 | Installation 3 | ============ 4 | 5 | At the command line:: 6 | 7 | $ easy_install outrigger 8 | 9 | Or, if you have virtualenvwrapper installed:: 10 | 11 | $ mkvirtualenv outrigger 12 | $ pip install outrigger 13 | -------------------------------------------------------------------------------- /docs/releases/template.rst: -------------------------------------------------------------------------------- 1 | v0.3.0 (...) 2 | ------------ 3 | 4 | This is the second release of `outrigger` 5 | 6 | New features 7 | ~~~~~~~~~~~~ 8 | 9 | - Parallelized exon finding for novel exons 10 | - Added ``outrigger validate`` command for 11 | 12 | Plotting functions 13 | ~~~~~~~~~~~~~~~~~~ 14 | 15 | API changes 16 | ~~~~~~~~~~~ 17 | 18 | 19 | Bug fixes 20 | ~~~~~~~~~ 21 | 22 | Miscellaneous 23 | ~~~~~~~~~~~~~ 24 | 25 | -------------------------------------------------------------------------------- /docs/releases/v0.1.0.rst: -------------------------------------------------------------------------------- 1 | v0.1.0 (May 25, 2016) 2 | --------------------- 3 | 4 | This is the initial release of ``outrigger`` 5 | -------------------------------------------------------------------------------- /docs/releases/v0.2.0.rst: -------------------------------------------------------------------------------- 1 | v0.2.0 (September 9th, 2016) 2 | ---------------------------- 3 | 4 | This is the second release of ``outrigger``! 5 | 6 | New features 7 | ~~~~~~~~~~~~ 8 | 9 | - Parallelized exon finding for novel exons 10 | - Added ``outrigger validate`` command to check that your new exons have proper splice sites (e.g. GT/AG and AT/AC) 11 | - Added more test data for other event types (even though we don't detect them yet) 12 | -------------------------------------------------------------------------------- /docs/releases/v0.2.1.rst: -------------------------------------------------------------------------------- 1 | v0.2.1 (September 12th, 2016) 2 | ----------------------------- 3 | 4 | This is a point release which actually includes the ``requirements.txt`` file that specifies which packages ``outrigger`` depends on. 5 | -------------------------------------------------------------------------------- /docs/releases/v0.2.2.rst: -------------------------------------------------------------------------------- 1 | v0.2.2 (September 12th, 2016) 2 | ----------------------------- 3 | 4 | This is a point release which includes the ``index`` submodule in the ``__all__`` statement. 5 | -------------------------------------------------------------------------------- /docs/releases/v0.2.3.rst: -------------------------------------------------------------------------------- 1 | v0.2.3 (September 13th, 2016) 2 | ----------------------------- 3 | 4 | This is a patch release of outrigger, with non-breaking changes from the 5 | previous one. 6 | 7 | Bug fixes 8 | ~~~~~~~~~ 9 | 10 | - Subfolders get copied when installing 11 | - Add test for checking that ``outrigger -h`` command works 12 | -------------------------------------------------------------------------------- /docs/releases/v0.2.4.rst: -------------------------------------------------------------------------------- 1 | v0.2.4 (September 14th, 2016) 2 | ----------------------------- 3 | 4 | This is a non-breaking patch release of ``outrigger``. 5 | 6 | New features 7 | ~~~~~~~~~~~~ 8 | 9 | - **Actually** parallelized exon finding for novel exons. Before had written the code and tested the non-parallelized version but now using actually parallelized version! 10 | 11 | 12 | Bug fixes 13 | ~~~~~~~~~ 14 | 15 | - Don't need to turn on ``--debug`` command for outrigger to even run 16 | 17 | -------------------------------------------------------------------------------- /docs/releases/v0.2.5.rst: -------------------------------------------------------------------------------- 1 | v0.2.5 (September 14th, 2016) 2 | ----------------------------- 3 | 4 | 5 | Bug fixes 6 | ~~~~~~~~~ 7 | 8 | - Added ``joblib`` to requirements 9 | -------------------------------------------------------------------------------- /docs/releases/v0.2.6.rst: -------------------------------------------------------------------------------- 1 | v0.2.6 (September 15th, 2016) 2 | ----------------------------- 3 | 4 | This is a non-breaking patch release 5 | 6 | Bug fixes 7 | ~~~~~~~~~ 8 | 9 | - Wasn't concatenating exons properly after parallelizing 10 | 11 | 12 | Miscellaneous 13 | ~~~~~~~~~~~~~ 14 | 15 | - Clarified ``.gtf`` file example for directory output 16 | -------------------------------------------------------------------------------- /docs/releases/v0.2.7.rst: -------------------------------------------------------------------------------- 1 | v0.2.7 (...) 2 | ------------ 3 | 4 | 5 | New features 6 | ~~~~~~~~~~~~ 7 | 8 | 9 | Plotting functions 10 | ~~~~~~~~~~~~~~~~~~ 11 | 12 | API changes 13 | ~~~~~~~~~~~ 14 | 15 | 16 | Bug fixes 17 | ~~~~~~~~~ 18 | 19 | Miscellaneous 20 | ~~~~~~~~~~~~~ 21 | 22 | - Added version info with ``outrigger --version`` 23 | - Add more indentation for sub-items of searching for new exons 24 | - Get intron and exon lengths at the same time as the GTF attributes to avoid 25 | performing a giant database merge 26 | -------------------------------------------------------------------------------- /docs/releases/v0.2.8.rst: -------------------------------------------------------------------------------- 1 | v0.2.8 (October 23rd, 2016) 2 | --------------------------- 3 | 4 | Updated README/HISTORY files 5 | -------------------------------------------------------------------------------- /docs/releases/v0.2.9.rst: -------------------------------------------------------------------------------- 1 | v0.2.9 (November 11th, 2016) 2 | ---------------------------- 3 | 4 | This is a non-breaking release with many speed improvements, and upgrade is 5 | recommended. 6 | 7 | 8 | New features 9 | ~~~~~~~~~~~~ 10 | 11 | - Add ``bam`` alignment files as input option 12 | 13 | 14 | Miscellaneous 15 | ~~~~~~~~~~~~~ 16 | 17 | - Parallelized Psi calculation, the exact number of processors can be specified with ``--n-jobs``, and by default, ``--n-jobs`` is ``-1``, which means use as many processors as are available. 18 | -------------------------------------------------------------------------------- /docs/releases/v1.0.0.rst: -------------------------------------------------------------------------------- 1 | v1.0.0 (April 3rd, 2017) 2 | ------------------------ 3 | 4 | This is the first major release of ``outrigger``!!! 5 | 6 | New features 7 | ~~~~~~~~~~~~ 8 | 9 | - Parallelized event across chromosomes 10 | - Added ``--low-memory`` flag for ``index``, ``validate``, and ``psi`` commands 11 | to use a smaller memory footprint when reading CSV files. 12 | - Added ``--splice-types`` option to specify only one kind of splicing you'd 13 | like to find 14 | - So the user can double-check the Psi calculation, create a ``summary.csv`` 15 | file indicating the number of reads found at each junction, for all samples 16 | - This also shows which "Case" corresponds to each event in each sample, so 17 | you can see whether there were sufficient or insufficient reads on the 18 | junctions of each event, and how ``outrigger`` judged it. 19 | - Added functions to extract constitutive and alternative exons separately 20 | 21 | Bug fixes 22 | ~~~~~~~~~ 23 | 24 | - Fixed a bug that stalled on ``.bam`` files while counting the junctions 25 | 26 | Miscellaneous 27 | ~~~~~~~~~~~~~ 28 | 29 | - Added ``GC/AG`` to valid splice sites 30 | -------------------------------------------------------------------------------- /docs/releases/v1.1.0.rst: -------------------------------------------------------------------------------- 1 | v1.1.0 (June 28th, 2017) 2 | ------------------------ 3 | 4 | This is a minor release to ```outrigger``. 5 | 6 | Bug fixes 7 | ~~~~~~~~~ 8 | 9 | - Fixed `UNIQUE ID` error that happened somewhat stochastically when adding new exons to the database 10 | 11 | 12 | Miscellaneous 13 | ~~~~~~~~~~~~~ 14 | 15 | - Explicitly added Python 3.6 compatibility 16 | - Change logo location to `logo/` instead of `logo/v1` since there's only one 17 | version anyway... 18 | -------------------------------------------------------------------------------- /docs/requirements.txt: -------------------------------------------------------------------------------- 1 | sphinx 2 | numpydoc 3 | -------------------------------------------------------------------------------- /docs/rsync_exclude: -------------------------------------------------------------------------------- 1 | .git 2 | -------------------------------------------------------------------------------- /docs/test_transcripts.png: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/YeoLab/outrigger/9da86d2d8d137b309a53cae8851ba867cf757201/docs/test_transcripts.png -------------------------------------------------------------------------------- /docs/tutorial.rst: -------------------------------------------------------------------------------- 1 | .. _tutorial: 2 | 3 | Flotilla tutorial 4 | ================= 5 | 6 | Installation 7 | ------------ 8 | 9 | .. toctree:: 10 | :maxdepth: 2 11 | 12 | installation 13 | 14 | Beginning examples 15 | ------------------ 16 | 17 | .. toctree:: 18 | :maxdepth: 1 19 | 20 | tutorial/barebones_study_making 21 | 22 | Advanced examples 23 | ----------------- 24 | 25 | .. toctree:: 26 | :maxdepth: 1 27 | 28 | tutorial/modalities 29 | 30 | Day to day helpful tips 31 | ----------------------- 32 | 33 | .. toctree:: 34 | :maxdepth: 2 35 | 36 | tutorial/supplementaldata 37 | 38 | 39 | .. Plotting functions 40 | ------------------ 41 | .. toctree:: 42 | :maxdepth: 1 43 | tutorial/pca 44 | tutorial/classification 45 | tutorial/network 46 | tutorial/expression_specific 47 | tutorial/splicing_specific 48 | 49 | Recreated papers 50 | ---------------- 51 | 52 | .. toctree:: 53 | :maxdepth: 1 54 | 55 | tutorial/shalek2013 56 | -------------------------------------------------------------------------------- /docs/usage.rst: -------------------------------------------------------------------------------- 1 | ===== 2 | Usage 3 | ===== 4 | 5 | To use ``outrigger``, you must perform at least steps 1 and 3: 6 | 7 | 1. ``outrigger index`` to read all your junctions in and create a database of alternatively spliced exons. 8 | 2. ``outrigger validate`` to filter your splicing events for only those with valid introns. (optional) 9 | 3. ``outrigger psi`` to calculate percent spliced in on your splicing events. 10 | 11 | |OutriggerOverview| 12 | 13 | .. |OutriggerOverview| image:: _static/outrigger_overview-300ppi.png 14 | :target: _static/outrigger_overview-300ppi.png 15 | 16 | 17 | Each of these commands deserves its own page of explanation, so look at the links below. 18 | 19 | Contents: 20 | 21 | .. toctree:: 22 | :maxdepth: 2 23 | 24 | subcommands/outrigger_index.rst 25 | subcommands/outrigger_validate.rst 26 | subcommands/outrigger_psi.rst 27 | -------------------------------------------------------------------------------- /environment.yml: -------------------------------------------------------------------------------- 1 | name: outrigger-env 2 | channels: 3 | - conda-forge 4 | - r 5 | - bioconda 6 | dependencies: 7 | - python=3 8 | - pytest 9 | - pandas>=0.17.0 10 | - coverage 11 | - gffutils 12 | - pybedtools 13 | - biopython 14 | - bedtools 15 | - joblib 16 | - pysam 17 | - sphinx>=1.3.6 18 | - sphinx_rtd_theme 19 | - pip: 20 | - graphlite 21 | - recommonmark==0.4.0 22 | - nbsphinx 23 | -------------------------------------------------------------------------------- /logo/logo-150ppi.png: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/YeoLab/outrigger/9da86d2d8d137b309a53cae8851ba867cf757201/logo/logo-150ppi.png -------------------------------------------------------------------------------- /logo/logo-1x.png: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/YeoLab/outrigger/9da86d2d8d137b309a53cae8851ba867cf757201/logo/logo-1x.png -------------------------------------------------------------------------------- /logo/logo-300ppi.png: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/YeoLab/outrigger/9da86d2d8d137b309a53cae8851ba867cf757201/logo/logo-300ppi.png 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home: https://github.com/YeoLab/outrigger 28 | summary: Create a *de novo* alternative splicing database, validate splicing events, and quantify percent spliced-in (Psi) from RNA seq data 29 | license: BSD 3-Clause 30 | -------------------------------------------------------------------------------- /outrigger/__init__.py: -------------------------------------------------------------------------------- 1 | # -*- coding: utf-8 -*- 2 | 3 | __author__ = 'Olga Botvinnik' 4 | __email__ = 'olga.botvinnik@gmail.com' 5 | __version__ = '1.1.1' 6 | 7 | __all__ = ['psi', 'region', 'util', 'io', 'validate', 'index', 8 | 'common'] 9 | -------------------------------------------------------------------------------- /outrigger/index/__init__.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/YeoLab/outrigger/9da86d2d8d137b309a53cae8851ba867cf757201/outrigger/index/__init__.py 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/outrigger/tests/data/simulated/outrigger_output/index/mxe/events_negative_strand.csv: -------------------------------------------------------------------------------- 1 | event_id,exon1,exon2,exon3,exon4,junction13,junction34,junction12,junction24,exons,junctions,strand,incompatible_junctions 2 | isoform1=junction:chr1:251-399:-@exon:chr1:225-250:-@junction:chr1:176-224:-|isoform2=junction:chr1:351-399:-@exon:chr1:300-350:-@junction:chr1:176-299:-,exon:chr1:400-425:-,exon:chr1:300-350:-,exon:chr1:225-250:-,exon:chr1:150-175:-,junction:chr1:251-399:-,junction:chr1:176-224:-,junction:chr1:351-399:-,junction:chr1:176-299:-,exon:chr1:400-425:-@exon:chr1:300-350:-@exon:chr1:225-250:-@exon:chr1:150-175:-,junction:chr1:251-399:-@junction:chr1:176-224:-@junction:chr1:351-399:-@junction:chr1:176-299:-,-,junction:chr1:176-399:-|junction:chr1:251-299:- 3 | -------------------------------------------------------------------------------- /outrigger/tests/data/simulated/outrigger_output/index/mxe/events_positive_strand.csv: -------------------------------------------------------------------------------- 1 | event_id,exon1,exon2,exon3,exon4,junction13,junction34,junction12,junction24,exons,junctions,strand,incompatible_junctions 2 | isoform1=junction:chr1:176-299:+@exon:chr1:300-350:+@junction:chr1:351-399:+|isoform2=junction:chr1:176-224:+@exon:chr1:225-250:+@junction:chr1:251-399:+,exon:chr1:150-175:+,exon:chr1:225-250:+,exon:chr1:300-350:+,exon:chr1:400-425:+,junction:chr1:176-299:+,junction:chr1:351-399:+,junction:chr1:176-224:+,junction:chr1:251-399:+,exon:chr1:150-175:+@exon:chr1:225-250:+@exon:chr1:300-350:+@exon:chr1:400-425:+,junction:chr1:176-299:+@junction:chr1:351-399:+@junction:chr1:176-224:+@junction:chr1:251-399:+,+,junction:chr1:176-399:+|junction:chr1:251-299:+ 3 | -------------------------------------------------------------------------------- /outrigger/tests/data/simulated/psi/mutually_exclusive_exon_junctions_psi.csv: -------------------------------------------------------------------------------- 1 | title,junction13,junction34,junction12,junction24,mean_psi,min_psi,case 2 | all zero,0,0,0,0,NA,NA,Case 2 3 | all insufficient,2,2,2,2,NA,NA,Case 3 4 | junction13 ≥ 10; junction12;24;34 < 10; ∑ < 40,10,2,2,2,NA,NA,Case 4 5 | junction12;13 ≥ 10; junction24;34 < 10; ∑ ≥ 40,20,2,9,2,NA,NA,Case 4 6 | "junction12;24;13;34 ≥ 10, junction24>>12",10,10,10,200,NA,NA,Case 5 7 | junction12;13;34 ≥ 10,10,10,10,0,NA,NA,Case 5 8 | junction13;34 ≥ 10,0,0,10,10,0,0,Case 6 9 | junction12;24 ≥ 10,10,10,0,0,1,1,Case 7 10 | junction12;24;13;34 ≥ 10,10,10,10,10,0.5,0.5,Case 8 11 | junction12;13;34 ≥ 10; junction24 < 10; ∑ ≥ 40; ∑min < 20,50,10,10,2,0.098,NA,Case 9a 12 | junction12;13;34 ≥ 10; junction24 < 10; ∑ ≥ 40; ∑min ≥ 20,100,100,10,2,0.057,0.02,"Case 9a, min" 13 | junction12;13;34 ≥ 10; junction24 < 10; ∑ < 40,10,10,10,2,NA,NA,Case 9b 14 | junction12;13 ≥ 10; junction24;34 < 10; ∑ ≥ 40,10,2,50,10,0.8333333333,NA,Case 10a 15 | junction13 ≥ 10; junction12;24;34 < 10; ∑ ≥ 40,10,2,10,10,NA,NA,Case 10b 16 | junction12;13 ≥ 10; junction24;34 < 10; ∑ ≥ 40,20,2,20,2,0.5,NA,Case 11a 17 | junction12;13 ≥ 10; junction24;34 < 10; ∑ < 40,10,2,10,2,NA,NA,Case 11b 18 | junction12;13 >> 10; ∑ ≥ 40,100,0,100,0,NA,NA,Case 4 -------------------------------------------------------------------------------- /outrigger/tests/data/simulated/unprocessed/true_splice_junctions.csv: -------------------------------------------------------------------------------- 1 | chrom,junction_start,junction_stop,strand,junction_motif,annotated,unique_junction_reads,multimap_junction_reads,max_overhang,exon_start,exon_stop,junction_id 2 | chr1,76,299,+,GT/AG,True,0,1,39,300,75,junction:chr1:76-299:+ 3 | chr1,201,299,+,GT/AG,True,0,1,10,300,200,junction:chr1:201-299:+ 4 | chr1,201,249,+,GT/AG,False,0,1,22,250,200,junction:chr1:201-249:+ 5 | chr1,201,799,+,GT/AG,True,19,20,43,800,200,junction:chr1:201-799:+ 6 | chr1,201,799,+,GT/AG,False,8,15,41,800,200,junction:chr1:201-799:+ 7 | chr1,155832,164262,+,GT/AG,True,61,3,46,164263,155831,junction:chr1:155832-164262:+ 8 | chr1,156087,156200,+,GT/AG,False,1,14,44,156201,156086,junction:chr1:156087-156200:+ 9 | chr1,329977,334128,+,GT/AG,True,0,2,14,334129,329976,junction:chr1:329977-334128:+ 10 | chr1,569184,569583,+,GT/AG,False,0,1,17,569584,569183,junction:chr1:569184-569583:+ 11 | chr1,655581,659737,+,GT/AG,True,0,2,14,659738,655580,junction:chr1:655581-659737:+ 12 | chr1,661725,662046,+,GT/AG,False,0,1,22,662047,661724,junction:chr1:661725-662046:+ 13 | chr1,668587,671992,+,GT/AG,False,0,4,28,671993,668586,junction:chr1:668587-671992:+ 14 | -------------------------------------------------------------------------------- /outrigger/tests/data/simulated/validate_negative_control/chromsizes: -------------------------------------------------------------------------------- 1 | simulated 1000 2 | -------------------------------------------------------------------------------- /outrigger/tests/data/simulated/validate_negative_control/exon2_downstream_splice_sites.csv: -------------------------------------------------------------------------------- 1 | isoform1=junction:simulated:150-500:+|isoform2=junction:simulated:150-300:+@exon:simulated:300-400:+@junction:simulated:400-500:+,AT 2 | isoform1=junction:simulated:100-600:-|isoform2=junction:simulated:300-600:-@exon:simulated:300-400:-@junction:simulated:100-400:-,TT 3 | -------------------------------------------------------------------------------- /outrigger/tests/data/simulated/validate_negative_control/exon2_upstream_splice_sites.csv: -------------------------------------------------------------------------------- 1 | isoform1=junction:simulated:150-500:+|isoform2=junction:simulated:150-300:+@exon:simulated:300-400:+@junction:simulated:400-500:+,AA 2 | isoform1=junction:simulated:100-600:-|isoform2=junction:simulated:300-600:-@exon:simulated:300-400:-@junction:simulated:100-400:-,AT 3 | -------------------------------------------------------------------------------- /outrigger/tests/data/simulated/validate_negative_control/genome.docx: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/YeoLab/outrigger/9da86d2d8d137b309a53cae8851ba867cf757201/outrigger/tests/data/simulated/validate_negative_control/genome.docx -------------------------------------------------------------------------------- /outrigger/tests/data/simulated/validate_negative_control/genome.fasta: -------------------------------------------------------------------------------- 1 | >simulated 2 | CATACGGCTTTGTACTGAGTACGGAGCCTCGGTGCTATGGACGTAAGCAACACTCGATCG 3 | CGCTGAGGGACCCTCTTTCAGGGACCTGCCTGGATAGTTGTCCGCGAACCGTGGCAGGAT 4 | GATACAGTGTCAATACTGAGGCCGGACAGGTGCGTCCCGCCCCGAAGGCGTATCGAATTA 5 | TGAGGTGGCGGGCAAAGGACGTCGAGTTGCCAACTATGTCTACAAACTGGGAAGAAAATC 6 | AGTTGTACCAGCAAACCGCGCTTGATAGAGCTCTGTTAGTTGGAAGCTATCCGGCAATAA 7 | CTCTGTGGCAAGCATTACAAACCATCGAACAGCGTTCTCCCAGACGATCGGGTAAGAACA 8 | GTAGCCTGCTGATGCGTATTGGCTCTCACTTAGCCGATTTATTGACAAGACGATAGAACT 9 | TCCTGAGCACACATTCCGGCTTAGGACAGAGAAACGTTGATCATGTGATTCGTAAGTTCG 10 | ATGGAGGCTATGTCGTATGCCAGAACCAGCGGTCGAGTTATTCATCACTGAGTCCCTGAA 11 | CCCACTAACGGTTTCCTTACACTATGAGTCGTCGGGTAGGTGTCTGGTCTAGTTGCGACG 12 | GAGCCGCCTTCCTTCATGACGATAGTCAGACGGAGGATGGCGTGCTTGTGACTCCGTTTG 13 | ATACAGACGCCATACAGTAGGAGACTGGAGGTAACTTAAATCCACCGGTGATAGCGTGCT 14 | GCTATTCAAACAAATGCCCTCATCCACAGCAGGCGTTGAGCAGACATTAATCTCAGCTGT 15 | ATGCGATCCCTACACCGGCTAGTGGGGGTCTTGTTGTCTCGGAGACTAAGACCTGAATGC 16 | CACCTCCCGGCCTGGTGAGCGATCTTACTGCCGACCTGTGGCGGCATCCCTTCAGAAACG 17 | CGAGCACCCTTGCTCTATTCACGAAGCGTAGGTGCCCTATTATTAATCGATCCTTCAGCA 18 | TAACCTGTGCTGTAACGGAAGACATGGAACCGCGTAGATC 19 | -------------------------------------------------------------------------------- /outrigger/tests/data/simulated/validate_negative_control/genome.fasta.fai: -------------------------------------------------------------------------------- 1 | simulated 1000 11 60 61 2 | -------------------------------------------------------------------------------- /outrigger/tests/data/simulated/validate_negative_control/outrigger_output/index/mxe/events.csv: -------------------------------------------------------------------------------- 1 | isoform1=junction:simulated:150-500:+@exon:simulated:300-400:+@junction:simulated:600-700:+|isoform2=junction:simulated:150-300:+@exon:simulated:300-400:+@junction:simulated:400-700:+ 2 | isoform1=junction:simulated:500-850:-@exon:simulated:300-400:-@junction:simulated:100-600:-|isoform2=junction:simulated:300-850:-@exon:simulated:300-400:-@junction:simulated:100-400:- -------------------------------------------------------------------------------- /outrigger/tests/data/simulated/validate_negative_control/outrigger_output/index/mxe/exon1.bed: -------------------------------------------------------------------------------- 1 | simulated 100 150 isoform1=junction:simulated:150-500:+@exon:simulated:300-400:+@junction:simulated:600-700:+|isoform2=junction:simulated:150-300:+@exon:simulated:300-400:+@junction:simulated:400-700:+ . + 2 | simulated 700 850 isoform1=junction:simulated:500-850:-@exon:simulated:300-400:-@junction:simulated:100-600:-|isoform2=junction:simulated:300-850:-@exon:simulated:300-400:-@junction:simulated:100-400:- . - 3 | -------------------------------------------------------------------------------- /outrigger/tests/data/simulated/validate_negative_control/outrigger_output/index/mxe/exon2.bed: -------------------------------------------------------------------------------- 1 | simulated 300 400 isoform1=junction:simulated:150-500:+@exon:simulated:300-400:+@junction:simulated:600-700:+|isoform2=junction:simulated:150-300:+@exon:simulated:300-400:+@junction:simulated:400-700:+ . + 2 | simulated 500 600 isoform1=junction:simulated:500-850:-@exon:simulated:300-400:-@junction:simulated:100-600:-|isoform2=junction:simulated:300-850:-@exon:simulated:300-400:-@junction:simulated:100-400:- . - 3 | -------------------------------------------------------------------------------- /outrigger/tests/data/simulated/validate_negative_control/outrigger_output/index/mxe/exon3.bed: -------------------------------------------------------------------------------- 1 | simulated 500 600 isoform1=junction:simulated:150-500:+@exon:simulated:300-400:+@junction:simulated:600-700:+|isoform2=junction:simulated:150-300:+@exon:simulated:300-400:+@junction:simulated:400-700:+ . + 2 | simulated 300 400 isoform1=junction:simulated:500-850:-@exon:simulated:300-400:-@junction:simulated:100-600:-|isoform2=junction:simulated:300-850:-@exon:simulated:300-400:-@junction:simulated:100-400:- . - 3 | -------------------------------------------------------------------------------- /outrigger/tests/data/simulated/validate_negative_control/outrigger_output/index/mxe/exon4.bed: -------------------------------------------------------------------------------- 1 | simulated 700 850 isoform1=junction:simulated:150-500:+@exon:simulated:300-400:+@junction:simulated:600-700:+|isoform2=junction:simulated:150-300:+@exon:simulated:300-400:+@junction:simulated:400-700:+ . + 2 | simulated 100 150 isoform1=junction:simulated:500-850:-@exon:simulated:300-400:-@junction:simulated:100-600:-|isoform2=junction:simulated:300-850:-@exon:simulated:300-400:-@junction:simulated:100-400:- . - 3 | -------------------------------------------------------------------------------- /outrigger/tests/data/simulated/validate_negative_control/outrigger_output/index/mxe/splice_sites.csv: -------------------------------------------------------------------------------- 1 | ,exon1-exon3_splice_site,exon3-exon4_splice_site,exon1-exon2_splice_site,exon2-exon4_splice_site 2 | isoform1=junction:simulated:150-500:+@exon:simulated:300-400:+@junction:simulated:600-700:+|isoform2=junction:simulated:150-300:+@exon:simulated:300-400:+@junction:simulated:400-700:+,TG/GC,GA/AA,TG/AA,AT/AA 3 | isoform1=junction:simulated:500-850:-@exon:simulated:300-400:-@junction:simulated:100-600:-|isoform2=junction:simulated:300-850:-@exon:simulated:300-400:-@junction:simulated:100-400:-,TT/AT,TT/CA,TT/TC,GC/CA 4 | -------------------------------------------------------------------------------- /outrigger/tests/data/simulated/validate_negative_control/outrigger_output/index/mxe/validated/events.csv: -------------------------------------------------------------------------------- 1 | isoform1=junction:simulated:150-500:+@exon:simulated:300-400:+@junction:simulated:600-700:+|isoform2=junction:simulated:150-300:+@exon:simulated:300-400:+@junction:simulated:400-700:+ 2 | -------------------------------------------------------------------------------- /outrigger/tests/data/simulated/validate_negative_control/outrigger_output/index/se/events.csv: -------------------------------------------------------------------------------- 1 | isoform1=junction:simulated:150-500:+|isoform2=junction:simulated:150-300:+@exon:simulated:300-400:+@junction:simulated:400-500:+ 2 | isoform1=junction:simulated:100-600:-|isoform2=junction:simulated:300-600:-@exon:simulated:300-400:-@junction:simulated:100-400:- -------------------------------------------------------------------------------- /outrigger/tests/data/simulated/validate_negative_control/outrigger_output/index/se/exon1.bed: -------------------------------------------------------------------------------- 1 | simulated 100 150 isoform1=junction:simulated:150-500:+|isoform2=junction:simulated:150-300:+@exon:simulated:300-400:+@junction:simulated:400-500:+ . + 2 | simulated 500 600 isoform1=junction:simulated:100-600:-|isoform2=junction:simulated:300-600:-@exon:simulated:300-400:-@junction:simulated:100-400:- . - 3 | -------------------------------------------------------------------------------- /outrigger/tests/data/simulated/validate_negative_control/outrigger_output/index/se/exon2.bed: -------------------------------------------------------------------------------- 1 | simulated 300 400 isoform1=junction:simulated:150-500:+|isoform2=junction:simulated:150-300:+@exon:simulated:300-400:+@junction:simulated:400-500:+ . + 2 | simulated 300 400 isoform1=junction:simulated:100-600:-|isoform2=junction:simulated:300-600:-@exon:simulated:300-400:-@junction:simulated:100-400:- . - 3 | -------------------------------------------------------------------------------- /outrigger/tests/data/simulated/validate_negative_control/outrigger_output/index/se/exon3.bed: -------------------------------------------------------------------------------- 1 | simulated 500 600 isoform1=junction:simulated:150-500:+|isoform2=junction:simulated:150-300:+@exon:simulated:300-400:+@junction:simulated:400-500:+ . + 2 | simulated 100 150 isoform1=junction:simulated:100-600:-|isoform2=junction:simulated:300-600:-@exon:simulated:300-400:-@junction:simulated:100-400:- . - 3 | -------------------------------------------------------------------------------- /outrigger/tests/data/simulated/validate_negative_control/outrigger_output/index/se/splice_sites.csv: -------------------------------------------------------------------------------- 1 | ,exon1-exon3_splice_site,exon1-exon2_splice_site,exon2-exon3_splice_site 2 | isoform1=junction:simulated:150-500:+|isoform2=junction:simulated:150-300:+@exon:simulated:300-400:+@junction:simulated:400-500:+,TG/GC,TG/AA,AT/GC 3 | isoform1=junction:simulated:100-600:-|isoform2=junction:simulated:300-600:-@exon:simulated:300-400:-@junction:simulated:100-400:-,GC/CA,GC/AT,TT/CA 4 | -------------------------------------------------------------------------------- /outrigger/tests/data/simulated/validate_negative_control/outrigger_output/index/se/validated/events.csv: -------------------------------------------------------------------------------- 1 | isoform1=junction:simulated:150-500:+|isoform2=junction:simulated:150-300:+@exon:simulated:300-400:+@junction:simulated:400-500:+ 2 | -------------------------------------------------------------------------------- /outrigger/tests/data/simulated/validate_negative_control/~$genome.docx: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/YeoLab/outrigger/9da86d2d8d137b309a53cae8851ba867cf757201/outrigger/tests/data/simulated/validate_negative_control/~$genome.docx -------------------------------------------------------------------------------- /outrigger/tests/data/tasic2016/intermediate/adjacent_junctions_single_exon.csv: -------------------------------------------------------------------------------- 1 | exon,direction,junction 2 | exon:chr2:136763573-136763621:+,downstream,junction:chr2:136758353-136763572:+ 3 | exon:chr2:136763573-136763621:+,upstream,junction:chr2:136763622-136766090:+ 4 | exon:chr2:136763573-136763621:+,upstream,junction:chr2:136763622-136766473:+ 5 | exon:chr2:136763573-136763621:+,upstream,junction:chr2:136763622-136769672:+ 6 | exon:chr2:136763573-136763621:+,upstream,junction:chr2:136763622-136769742:+ 7 | exon:chr2:136763573-136763621:+,upstream,junction:chr2:136763622-136770056:+ 8 | -------------------------------------------------------------------------------- /outrigger/tests/data/tasic2016/intermediate/single_junction_exon_triple.csv: -------------------------------------------------------------------------------- 1 | exon,direction,junction 2 | exon:chr2:136763573-136763621:+,downstream,junction:chr2:136763622-136766090:+ 3 | exon:chr2:136763573-136763621:+,downstream,junction:chr2:136763622-136766473:+ 4 | exon:chr2:136763573-136763621:+,downstream,junction:chr2:136763622-136769672:+ 5 | exon:chr2:136763573-136763621:+,downstream,junction:chr2:136763622-136769742:+ 6 | exon:chr2:136763573-136763621:+,downstream,junction:chr2:136763622-136770056:+ 7 | -------------------------------------------------------------------------------- /outrigger/tests/data/tasic2016/outrigger_output/index/gtf/gencode.vM10.annotation.subset.gtf.db: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/YeoLab/outrigger/9da86d2d8d137b309a53cae8851ba867cf757201/outrigger/tests/data/tasic2016/outrigger_output/index/gtf/gencode.vM10.annotation.subset.gtf.db -------------------------------------------------------------------------------- /outrigger/tests/data/tasic2016/outrigger_output/index/mxe/event.bed: -------------------------------------------------------------------------------- 1 | chr2 136763574 136774020 isoform1=junction:chr2:136763622-136770056:+@exon:chr2:136770057-136770174:+@junction:chr2:136770175-136773894:+|isoform2=junction:chr2:136763622-136769742:+@exon:chr2:136769743-136769860:+@junction:chr2:136769861-136773894:+ . + 2 | chr10 128490859 128492136 isoform1=junction:chr10:128491348-128492058:-@novel_exon:chr10:128491290-128491347:-@junction:chr10:128491034-128491289:-|isoform2=junction:chr10:128491765-128492058:-@novel_exon:chr10:128491720-128491764:-@junction:chr10:128491034-128491719:- . - 3 | chr2 136763572 136774020 isoform1=junction:chr2:136763622-136770056:+@exon:chr2:136770057-136770174:+@junction:chr2:136770175-136773894:+|isoform2=junction:chr2:136763622-136769742:+@exon:chr2:136769743-136769860:+@junction:chr2:136769861-136773894:+ . + 4 | -------------------------------------------------------------------------------- /outrigger/tests/data/tasic2016/outrigger_output/index/mxe/exon1.bed: -------------------------------------------------------------------------------- 1 | chr2 136763574 136763621 isoform1=junction:chr2:136763622-136770056:+@exon:chr2:136770057-136770174:+@junction:chr2:136770175-136773894:+|isoform2=junction:chr2:136763622-136769742:+@exon:chr2:136769743-136769860:+@junction:chr2:136769861-136773894:+ . + 2 | chr10 128492058 128492136 isoform1=junction:chr10:128491348-128492058:-@novel_exon:chr10:128491290-128491347:-@junction:chr10:128491034-128491289:-|isoform2=junction:chr10:128491765-128492058:-@novel_exon:chr10:128491720-128491764:-@junction:chr10:128491034-128491719:- . - 3 | chr2 136763572 136763621 isoform1=junction:chr2:136763622-136770056:+@exon:chr2:136770057-136770174:+@junction:chr2:136770175-136773894:+|isoform2=junction:chr2:136763622-136769742:+@exon:chr2:136769743-136769860:+@junction:chr2:136769861-136773894:+ . + 4 | -------------------------------------------------------------------------------- /outrigger/tests/data/tasic2016/outrigger_output/index/mxe/exon2.bed: -------------------------------------------------------------------------------- 1 | chr2 136769742 136769860 isoform1=junction:chr2:136763622-136770056:+@exon:chr2:136770057-136770174:+@junction:chr2:136770175-136773894:+|isoform2=junction:chr2:136763622-136769742:+@exon:chr2:136769743-136769860:+@junction:chr2:136769861-136773894:+ . + 2 | chr10 128491719 128491764 isoform1=junction:chr10:128491348-128492058:-@novel_exon:chr10:128491290-128491347:-@junction:chr10:128491034-128491289:-|isoform2=junction:chr10:128491765-128492058:-@novel_exon:chr10:128491720-128491764:-@junction:chr10:128491034-128491719:- . - 3 | chr2 136769742 136769860 isoform1=junction:chr2:136763622-136770056:+@exon:chr2:136770057-136770174:+@junction:chr2:136770175-136773894:+|isoform2=junction:chr2:136763622-136769742:+@exon:chr2:136769743-136769860:+@junction:chr2:136769861-136773894:+ . + 4 | -------------------------------------------------------------------------------- /outrigger/tests/data/tasic2016/outrigger_output/index/mxe/exon3.bed: -------------------------------------------------------------------------------- 1 | chr2 136770056 136770174 isoform1=junction:chr2:136763622-136770056:+@exon:chr2:136770057-136770174:+@junction:chr2:136770175-136773894:+|isoform2=junction:chr2:136763622-136769742:+@exon:chr2:136769743-136769860:+@junction:chr2:136769861-136773894:+ . + 2 | chr10 128491289 128491347 isoform1=junction:chr10:128491348-128492058:-@novel_exon:chr10:128491290-128491347:-@junction:chr10:128491034-128491289:-|isoform2=junction:chr10:128491765-128492058:-@novel_exon:chr10:128491720-128491764:-@junction:chr10:128491034-128491719:- . - 3 | chr2 136770056 136770174 isoform1=junction:chr2:136763622-136770056:+@exon:chr2:136770057-136770174:+@junction:chr2:136770175-136773894:+|isoform2=junction:chr2:136763622-136769742:+@exon:chr2:136769743-136769860:+@junction:chr2:136769861-136773894:+ . + 4 | -------------------------------------------------------------------------------- /outrigger/tests/data/tasic2016/outrigger_output/index/mxe/exon4.bed: -------------------------------------------------------------------------------- 1 | chr2 136773894 136774020 isoform1=junction:chr2:136763622-136770056:+@exon:chr2:136770057-136770174:+@junction:chr2:136770175-136773894:+|isoform2=junction:chr2:136763622-136769742:+@exon:chr2:136769743-136769860:+@junction:chr2:136769861-136773894:+ . + 2 | chr10 128490859 128491033 isoform1=junction:chr10:128491348-128492058:-@novel_exon:chr10:128491290-128491347:-@junction:chr10:128491034-128491289:-|isoform2=junction:chr10:128491765-128492058:-@novel_exon:chr10:128491720-128491764:-@junction:chr10:128491034-128491719:- . - 3 | chr2 136773894 136774020 isoform1=junction:chr2:136763622-136770056:+@exon:chr2:136770057-136770174:+@junction:chr2:136770175-136773894:+|isoform2=junction:chr2:136763622-136769742:+@exon:chr2:136769743-136769860:+@junction:chr2:136769861-136773894:+ . + 4 | -------------------------------------------------------------------------------- /outrigger/tests/data/tasic2016/outrigger_output/index/mxe/intron.bed: -------------------------------------------------------------------------------- 1 | chr2 136763620 136773895 isoform1=junction:chr2:136763622-136770056:+@exon:chr2:136770057-136770174:+@junction:chr2:136770175-136773894:+|isoform2=junction:chr2:136763622-136769742:+@exon:chr2:136769743-136769860:+@junction:chr2:136769861-136773894:+ . + 2 | chr10 128491032 128492059 isoform1=junction:chr10:128491348-128492058:-@novel_exon:chr10:128491290-128491347:-@junction:chr10:128491034-128491289:-|isoform2=junction:chr10:128491765-128492058:-@novel_exon:chr10:128491720-128491764:-@junction:chr10:128491034-128491719:- . - 3 | chr2 136763620 136773895 isoform1=junction:chr2:136763622-136770056:+@exon:chr2:136770057-136770174:+@junction:chr2:136770175-136773894:+|isoform2=junction:chr2:136763622-136769742:+@exon:chr2:136769743-136769860:+@junction:chr2:136769861-136773894:+ . + 4 | -------------------------------------------------------------------------------- /outrigger/tests/data/tasic2016/outrigger_output_bam/index/gtf/gencode.vM10.annotation.subset.gtf.db: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/YeoLab/outrigger/9da86d2d8d137b309a53cae8851ba867cf757201/outrigger/tests/data/tasic2016/outrigger_output_bam/index/gtf/gencode.vM10.annotation.subset.gtf.db -------------------------------------------------------------------------------- /outrigger/tests/data/tasic2016/outrigger_output_bam/index/gtf/novel_exons.gtf: -------------------------------------------------------------------------------- 1 | chr10 outrigger_de_novo novel_exon 128491720 128491764 . + . location_id "novel_exon:chr10:128491720-128491764:+"; 2 | chr10 outrigger_de_novo novel_exon 128492059 128492136 . + . location_id "novel_exon:chr10:128492059-128492136:+"; 3 | chr14 outrigger_de_novo novel_exon 24495430 24495449 . - . location_id "novel_exon:chr14:24495430-24495449:-"; 4 | chr14 outrigger_de_novo novel_exon 64313687 64313755 . - . location_id "novel_exon:chr14:64313687-64313755:-"; 5 | chr17 outrigger_de_novo novel_exon 80204313 80204387 . + . location_id "novel_exon:chr17:80204313-80204387:+"; 6 | chr9 outrigger_de_novo novel_exon 67031452 67031514 . + . location_id "novel_exon:chr9:67031452-67031514:+"; 7 | chr9 outrigger_de_novo novel_exon 67031951 67032026 . . . location_id "novel_exon:chr9:67031951-67032026:."; 8 | -------------------------------------------------------------------------------- /outrigger/tests/data/tasic2016/outrigger_output_bam/index/mxe/event.bed: -------------------------------------------------------------------------------- 1 | chr2 136763572 136774020 isoform1=junction:chr2:136763622-136770056:+@exon:chr2:136770057-136770174:+@junction:chr2:136770175-136773894:+|isoform2=junction:chr2:136763622-136769742:+@exon:chr2:136769743-136769860:+@junction:chr2:136769861-136773894:+ . + 2 | -------------------------------------------------------------------------------- /outrigger/tests/data/tasic2016/outrigger_output_bam/index/mxe/exon1.bed: -------------------------------------------------------------------------------- 1 | chr2 136763572 136763621 isoform1=junction:chr2:136763622-136770056:+@exon:chr2:136770057-136770174:+@junction:chr2:136770175-136773894:+|isoform2=junction:chr2:136763622-136769742:+@exon:chr2:136769743-136769860:+@junction:chr2:136769861-136773894:+ . + 2 | -------------------------------------------------------------------------------- /outrigger/tests/data/tasic2016/outrigger_output_bam/index/mxe/exon2.bed: -------------------------------------------------------------------------------- 1 | chr2 136769742 136769860 isoform1=junction:chr2:136763622-136770056:+@exon:chr2:136770057-136770174:+@junction:chr2:136770175-136773894:+|isoform2=junction:chr2:136763622-136769742:+@exon:chr2:136769743-136769860:+@junction:chr2:136769861-136773894:+ . + 2 | -------------------------------------------------------------------------------- /outrigger/tests/data/tasic2016/outrigger_output_bam/index/mxe/exon3.bed: -------------------------------------------------------------------------------- 1 | chr2 136770056 136770174 isoform1=junction:chr2:136763622-136770056:+@exon:chr2:136770057-136770174:+@junction:chr2:136770175-136773894:+|isoform2=junction:chr2:136763622-136769742:+@exon:chr2:136769743-136769860:+@junction:chr2:136769861-136773894:+ . + 2 | -------------------------------------------------------------------------------- /outrigger/tests/data/tasic2016/outrigger_output_bam/index/mxe/exon4.bed: -------------------------------------------------------------------------------- 1 | chr2 136773894 136774020 isoform1=junction:chr2:136763622-136770056:+@exon:chr2:136770057-136770174:+@junction:chr2:136770175-136773894:+|isoform2=junction:chr2:136763622-136769742:+@exon:chr2:136769743-136769860:+@junction:chr2:136769861-136773894:+ . + 2 | -------------------------------------------------------------------------------- /outrigger/tests/data/tasic2016/outrigger_output_bam/index/mxe/intron.bed: -------------------------------------------------------------------------------- 1 | chr2 136763620 136773895 isoform1=junction:chr2:136763622-136770056:+@exon:chr2:136770057-136770174:+@junction:chr2:136770175-136773894:+|isoform2=junction:chr2:136763622-136769742:+@exon:chr2:136769743-136769860:+@junction:chr2:136769861-136773894:+ . + 2 | -------------------------------------------------------------------------------- /outrigger/tests/data/tasic2016/outrigger_output_bam/index/se/event.bed: -------------------------------------------------------------------------------- 1 | chr16 84831328 84834832 isoform1=junction:chr16:84831508-84834808:-|isoform2=junction:chr16:84833875-84834808:-@exon:chr16:84833820-84833874:-@junction:chr16:84831508-84833819:- . - 2 | chr16 84831368 84834983 isoform1=junction:chr16:84831508-84834808:-|isoform2=junction:chr16:84833875-84834808:-@exon:chr16:84833820-84833874:-@junction:chr16:84831508-84833819:- . - 3 | chr16 84831368 84834832 isoform1=junction:chr16:84831508-84834808:-|isoform2=junction:chr16:84833875-84834808:-@exon:chr16:84833820-84833874:-@junction:chr16:84831508-84833819:- . - 4 | chr16 84831070 84834983 isoform1=junction:chr16:84831508-84834808:-|isoform2=junction:chr16:84833875-84834808:-@exon:chr16:84833820-84833874:-@junction:chr16:84831508-84833819:- . - 5 | chr16 84831368 84835298 isoform1=junction:chr16:84831508-84834808:-|isoform2=junction:chr16:84833875-84834808:-@exon:chr16:84833820-84833874:-@junction:chr16:84831508-84833819:- . - 6 | chr16 84831070 84834832 isoform1=junction:chr16:84831508-84834808:-|isoform2=junction:chr16:84833875-84834808:-@exon:chr16:84833820-84833874:-@junction:chr16:84831508-84833819:- . - 7 | chr16 84831070 84835298 isoform1=junction:chr16:84831508-84834808:-|isoform2=junction:chr16:84833875-84834808:-@exon:chr16:84833820-84833874:-@junction:chr16:84831508-84833819:- . - 8 | chr16 84831328 84834983 isoform1=junction:chr16:84831508-84834808:-|isoform2=junction:chr16:84833875-84834808:-@exon:chr16:84833820-84833874:-@junction:chr16:84831508-84833819:- . - 9 | chr16 84831328 84835298 isoform1=junction:chr16:84831508-84834808:-|isoform2=junction:chr16:84833875-84834808:-@exon:chr16:84833820-84833874:-@junction:chr16:84831508-84833819:- . - 10 | -------------------------------------------------------------------------------- /outrigger/tests/data/tasic2016/outrigger_output_bam/index/se/exon1.bed: -------------------------------------------------------------------------------- 1 | chr16 84834808 84834832 isoform1=junction:chr16:84831508-84834808:-|isoform2=junction:chr16:84833875-84834808:-@exon:chr16:84833820-84833874:-@junction:chr16:84831508-84833819:- . - 2 | chr16 84834808 84834983 isoform1=junction:chr16:84831508-84834808:-|isoform2=junction:chr16:84833875-84834808:-@exon:chr16:84833820-84833874:-@junction:chr16:84831508-84833819:- . - 3 | chr16 84834808 84834832 isoform1=junction:chr16:84831508-84834808:-|isoform2=junction:chr16:84833875-84834808:-@exon:chr16:84833820-84833874:-@junction:chr16:84831508-84833819:- . - 4 | chr16 84834808 84834983 isoform1=junction:chr16:84831508-84834808:-|isoform2=junction:chr16:84833875-84834808:-@exon:chr16:84833820-84833874:-@junction:chr16:84831508-84833819:- . - 5 | chr16 84834808 84835298 isoform1=junction:chr16:84831508-84834808:-|isoform2=junction:chr16:84833875-84834808:-@exon:chr16:84833820-84833874:-@junction:chr16:84831508-84833819:- . - 6 | chr16 84834808 84834832 isoform1=junction:chr16:84831508-84834808:-|isoform2=junction:chr16:84833875-84834808:-@exon:chr16:84833820-84833874:-@junction:chr16:84831508-84833819:- . - 7 | chr16 84834808 84835298 isoform1=junction:chr16:84831508-84834808:-|isoform2=junction:chr16:84833875-84834808:-@exon:chr16:84833820-84833874:-@junction:chr16:84831508-84833819:- . - 8 | chr16 84834808 84834983 isoform1=junction:chr16:84831508-84834808:-|isoform2=junction:chr16:84833875-84834808:-@exon:chr16:84833820-84833874:-@junction:chr16:84831508-84833819:- . - 9 | chr16 84834808 84835298 isoform1=junction:chr16:84831508-84834808:-|isoform2=junction:chr16:84833875-84834808:-@exon:chr16:84833820-84833874:-@junction:chr16:84831508-84833819:- . - 10 | -------------------------------------------------------------------------------- /outrigger/tests/data/tasic2016/outrigger_output_bam/index/se/exon2.bed: -------------------------------------------------------------------------------- 1 | chr16 84833819 84833874 isoform1=junction:chr16:84831508-84834808:-|isoform2=junction:chr16:84833875-84834808:-@exon:chr16:84833820-84833874:-@junction:chr16:84831508-84833819:- . - 2 | chr16 84833819 84833874 isoform1=junction:chr16:84831508-84834808:-|isoform2=junction:chr16:84833875-84834808:-@exon:chr16:84833820-84833874:-@junction:chr16:84831508-84833819:- . - 3 | chr16 84833819 84833874 isoform1=junction:chr16:84831508-84834808:-|isoform2=junction:chr16:84833875-84834808:-@exon:chr16:84833820-84833874:-@junction:chr16:84831508-84833819:- . - 4 | chr16 84833819 84833874 isoform1=junction:chr16:84831508-84834808:-|isoform2=junction:chr16:84833875-84834808:-@exon:chr16:84833820-84833874:-@junction:chr16:84831508-84833819:- . - 5 | chr16 84833819 84833874 isoform1=junction:chr16:84831508-84834808:-|isoform2=junction:chr16:84833875-84834808:-@exon:chr16:84833820-84833874:-@junction:chr16:84831508-84833819:- . - 6 | chr16 84833819 84833874 isoform1=junction:chr16:84831508-84834808:-|isoform2=junction:chr16:84833875-84834808:-@exon:chr16:84833820-84833874:-@junction:chr16:84831508-84833819:- . - 7 | chr16 84833819 84833874 isoform1=junction:chr16:84831508-84834808:-|isoform2=junction:chr16:84833875-84834808:-@exon:chr16:84833820-84833874:-@junction:chr16:84831508-84833819:- . - 8 | chr16 84833819 84833874 isoform1=junction:chr16:84831508-84834808:-|isoform2=junction:chr16:84833875-84834808:-@exon:chr16:84833820-84833874:-@junction:chr16:84831508-84833819:- . - 9 | chr16 84833819 84833874 isoform1=junction:chr16:84831508-84834808:-|isoform2=junction:chr16:84833875-84834808:-@exon:chr16:84833820-84833874:-@junction:chr16:84831508-84833819:- . - 10 | -------------------------------------------------------------------------------- /outrigger/tests/data/tasic2016/outrigger_output_bam/index/se/exon3.bed: -------------------------------------------------------------------------------- 1 | chr16 84831328 84831507 isoform1=junction:chr16:84831508-84834808:-|isoform2=junction:chr16:84833875-84834808:-@exon:chr16:84833820-84833874:-@junction:chr16:84831508-84833819:- . - 2 | chr16 84831368 84831507 isoform1=junction:chr16:84831508-84834808:-|isoform2=junction:chr16:84833875-84834808:-@exon:chr16:84833820-84833874:-@junction:chr16:84831508-84833819:- . - 3 | chr16 84831368 84831507 isoform1=junction:chr16:84831508-84834808:-|isoform2=junction:chr16:84833875-84834808:-@exon:chr16:84833820-84833874:-@junction:chr16:84831508-84833819:- . - 4 | chr16 84831070 84831507 isoform1=junction:chr16:84831508-84834808:-|isoform2=junction:chr16:84833875-84834808:-@exon:chr16:84833820-84833874:-@junction:chr16:84831508-84833819:- . - 5 | chr16 84831368 84831507 isoform1=junction:chr16:84831508-84834808:-|isoform2=junction:chr16:84833875-84834808:-@exon:chr16:84833820-84833874:-@junction:chr16:84831508-84833819:- . - 6 | chr16 84831070 84831507 isoform1=junction:chr16:84831508-84834808:-|isoform2=junction:chr16:84833875-84834808:-@exon:chr16:84833820-84833874:-@junction:chr16:84831508-84833819:- . - 7 | chr16 84831070 84831507 isoform1=junction:chr16:84831508-84834808:-|isoform2=junction:chr16:84833875-84834808:-@exon:chr16:84833820-84833874:-@junction:chr16:84831508-84833819:- . - 8 | chr16 84831328 84831507 isoform1=junction:chr16:84831508-84834808:-|isoform2=junction:chr16:84833875-84834808:-@exon:chr16:84833820-84833874:-@junction:chr16:84831508-84833819:- . - 9 | chr16 84831328 84831507 isoform1=junction:chr16:84831508-84834808:-|isoform2=junction:chr16:84833875-84834808:-@exon:chr16:84833820-84833874:-@junction:chr16:84831508-84833819:- . - 10 | -------------------------------------------------------------------------------- /outrigger/tests/data/tasic2016/outrigger_output_bam/index/se/intron.bed: -------------------------------------------------------------------------------- 1 | chr16 84831506 84834809 isoform1=junction:chr16:84831508-84834808:-|isoform2=junction:chr16:84833875-84834808:-@exon:chr16:84833820-84833874:-@junction:chr16:84831508-84833819:- . - 2 | chr16 84831506 84834809 isoform1=junction:chr16:84831508-84834808:-|isoform2=junction:chr16:84833875-84834808:-@exon:chr16:84833820-84833874:-@junction:chr16:84831508-84833819:- . - 3 | chr16 84831506 84834809 isoform1=junction:chr16:84831508-84834808:-|isoform2=junction:chr16:84833875-84834808:-@exon:chr16:84833820-84833874:-@junction:chr16:84831508-84833819:- . - 4 | chr16 84831506 84834809 isoform1=junction:chr16:84831508-84834808:-|isoform2=junction:chr16:84833875-84834808:-@exon:chr16:84833820-84833874:-@junction:chr16:84831508-84833819:- . - 5 | chr16 84831506 84834809 isoform1=junction:chr16:84831508-84834808:-|isoform2=junction:chr16:84833875-84834808:-@exon:chr16:84833820-84833874:-@junction:chr16:84831508-84833819:- . - 6 | chr16 84831506 84834809 isoform1=junction:chr16:84831508-84834808:-|isoform2=junction:chr16:84833875-84834808:-@exon:chr16:84833820-84833874:-@junction:chr16:84831508-84833819:- . - 7 | chr16 84831506 84834809 isoform1=junction:chr16:84831508-84834808:-|isoform2=junction:chr16:84833875-84834808:-@exon:chr16:84833820-84833874:-@junction:chr16:84831508-84833819:- . - 8 | chr16 84831506 84834809 isoform1=junction:chr16:84831508-84834808:-|isoform2=junction:chr16:84833875-84834808:-@exon:chr16:84833820-84833874:-@junction:chr16:84831508-84833819:- . - 9 | chr16 84831506 84834809 isoform1=junction:chr16:84831508-84834808:-|isoform2=junction:chr16:84833875-84834808:-@exon:chr16:84833820-84833874:-@junction:chr16:84831508-84833819:- . - 10 | -------------------------------------------------------------------------------- /outrigger/tests/data/tasic2016/outrigger_output_bam/psi/mxe/psi.csv: -------------------------------------------------------------------------------- 1 | sample_id,isoform1=junction:chr2:136763622-136770056:+@exon:chr2:136770057-136770174:+@junction:chr2:136770175-136773894:+|isoform2=junction:chr2:136763622-136769742:+@exon:chr2:136769743-136769860:+@junction:chr2:136769861-136773894:+ 2 | CAV_LP_Ipsi_tdTpos_cell_1-SRR2140356-GSM1840944_R1.polyATrim.adapterTrim.rmRep.sorted.rg.subset.sorted.bam,0.37802702013764977 3 | CAV_LP_Ipsi_tdTpos_cell_2-SRR2140357-GSM1840945_R1.polyATrim.adapterTrim.rmRep.sorted.rg.subset.sorted.bam,0.37802702013764977 4 | -------------------------------------------------------------------------------- /outrigger/tests/data/tasic2016/outrigger_output_bam/psi/mxe/summary.csv: -------------------------------------------------------------------------------- 1 | sample_id,event_id,isoform1_junction13,isoform1_junction34,isoform2_junction12,isoform2_junction24,psi,notes 2 | CAV_LP_Ipsi_tdTpos_cell_1-SRR2140356-GSM1840944_R1.polyATrim.adapterTrim.rmRep.sorted.rg.subset.sorted.bam,isoform1=junction:chr2:136763622-136770056:+@exon:chr2:136770057-136770174:+@junction:chr2:136770175-136773894:+|isoform2=junction:chr2:136763622-136769742:+@exon:chr2:136769743-136769860:+@junction:chr2:136769861-136773894:+,1279.0,1161.0,734.0,749.0,0.37802702013764977,Case 5: Sufficient coverage on both isoforms 3 | CAV_LP_Ipsi_tdTpos_cell_2-SRR2140357-GSM1840945_R1.polyATrim.adapterTrim.rmRep.sorted.rg.subset.sorted.bam,isoform1=junction:chr2:136763622-136770056:+@exon:chr2:136770057-136770174:+@junction:chr2:136770175-136773894:+|isoform2=junction:chr2:136763622-136769742:+@exon:chr2:136769743-136769860:+@junction:chr2:136769861-136773894:+,1279.0,1161.0,734.0,749.0,0.37802702013764977,Case 5: Sufficient coverage on both isoforms 4 | -------------------------------------------------------------------------------- /outrigger/tests/data/tasic2016/outrigger_output_bam/psi/outrigger_psi.csv: -------------------------------------------------------------------------------- 1 | event_id,CAV_LP_Ipsi_tdTpos_cell_1-SRR2140356-GSM1840944_R1.polyATrim.adapterTrim.rmRep.sorted.rg.subset.sorted.bam,CAV_LP_Ipsi_tdTpos_cell_2-SRR2140357-GSM1840945_R1.polyATrim.adapterTrim.rmRep.sorted.rg.subset.sorted.bam 2 | isoform1=junction:chr16:84831508-84834808:-|isoform2=junction:chr16:84833875-84834808:-@exon:chr16:84833820-84833874:-@junction:chr16:84831508-84833819:-,0.14408973252804141,0.14408973252804141 3 | isoform1=junction:chr2:136763622-136770056:+@exon:chr2:136770057-136770174:+@junction:chr2:136770175-136773894:+|isoform2=junction:chr2:136763622-136769742:+@exon:chr2:136769743-136769860:+@junction:chr2:136769861-136773894:+,0.37802702013764977,0.37802702013764977 4 | -------------------------------------------------------------------------------- /outrigger/tests/data/tasic2016/outrigger_output_bam/psi/outrigger_summary.csv: -------------------------------------------------------------------------------- 1 | Unnamed: 0,event_id,isoform1_junction13,isoform1_junction34,isoform2_junction12,isoform2_junction23,isoform2_junction24,notes,psi,sample_id,splice_type 2 | 0,isoform1=junction:chr16:84831508-84834808:-|isoform2=junction:chr16:84833875-84834808:-@exon:chr16:84833820-84833874:-@junction:chr16:84831508-84833819:-,496,,89,78.0,,Case 8: Sufficient reads on all junctions,0.1440897325280414,CAV_LP_Ipsi_tdTpos_cell_1-SRR2140356-GSM1840944_R1.polyATrim.adapterTrim.rmRep.sorted.rg.subset.sorted.bam,se 3 | 1,isoform1=junction:chr16:84831508-84834808:-|isoform2=junction:chr16:84833875-84834808:-@exon:chr16:84833820-84833874:-@junction:chr16:84831508-84833819:-,496,,89,78.0,,Case 8: Sufficient reads on all junctions,0.1440897325280414,CAV_LP_Ipsi_tdTpos_cell_2-SRR2140357-GSM1840945_R1.polyATrim.adapterTrim.rmRep.sorted.rg.subset.sorted.bam,se 4 | 2,isoform1=junction:chr2:136763622-136770056:+@exon:chr2:136770057-136770174:+@junction:chr2:136770175-136773894:+|isoform2=junction:chr2:136763622-136769742:+@exon:chr2:136769743-136769860:+@junction:chr2:136769861-136773894:+,1279,1161.0,734,,749.0,Case 8: Sufficient reads on all junctions,0.37802702013764977,CAV_LP_Ipsi_tdTpos_cell_1-SRR2140356-GSM1840944_R1.polyATrim.adapterTrim.rmRep.sorted.rg.subset.sorted.bam,mxe 5 | 3,isoform1=junction:chr2:136763622-136770056:+@exon:chr2:136770057-136770174:+@junction:chr2:136770175-136773894:+|isoform2=junction:chr2:136763622-136769742:+@exon:chr2:136769743-136769860:+@junction:chr2:136769861-136773894:+,1279,1161.0,734,,749.0,Case 8: Sufficient reads on all junctions,0.37802702013764977,CAV_LP_Ipsi_tdTpos_cell_2-SRR2140357-GSM1840945_R1.polyATrim.adapterTrim.rmRep.sorted.rg.subset.sorted.bam,mxe 6 | -------------------------------------------------------------------------------- /outrigger/tests/data/tasic2016/outrigger_output_bam/psi/se/psi.csv: -------------------------------------------------------------------------------- 1 | sample_id,isoform1=junction:chr16:84831508-84834808:-|isoform2=junction:chr16:84833875-84834808:-@exon:chr16:84833820-84833874:-@junction:chr16:84831508-84833819:- 2 | CAV_LP_Ipsi_tdTpos_cell_1-SRR2140356-GSM1840944_R1.polyATrim.adapterTrim.rmRep.sorted.rg.subset.sorted.bam,0.14408973252804141 3 | CAV_LP_Ipsi_tdTpos_cell_2-SRR2140357-GSM1840945_R1.polyATrim.adapterTrim.rmRep.sorted.rg.subset.sorted.bam,0.14408973252804141 4 | -------------------------------------------------------------------------------- /outrigger/tests/data/tasic2016/outrigger_output_bam/psi/se/summary.csv: -------------------------------------------------------------------------------- 1 | sample_id,event_id,isoform1_junction13,isoform2_junction12,isoform2_junction23,psi,notes 2 | CAV_LP_Ipsi_tdTpos_cell_1-SRR2140356-GSM1840944_R1.polyATrim.adapterTrim.rmRep.sorted.rg.subset.sorted.bam,isoform1=junction:chr16:84831508-84834808:-|isoform2=junction:chr16:84833875-84834808:-@exon:chr16:84833820-84833874:-@junction:chr16:84831508-84833819:-,496.0,89.0,78.0,0.14408973252804141,Case 5: Sufficient coverage on both isoforms 3 | CAV_LP_Ipsi_tdTpos_cell_2-SRR2140357-GSM1840945_R1.polyATrim.adapterTrim.rmRep.sorted.rg.subset.sorted.bam,isoform1=junction:chr16:84831508-84834808:-|isoform2=junction:chr16:84833875-84834808:-@exon:chr16:84833820-84833874:-@junction:chr16:84831508-84833819:-,496.0,89.0,78.0,0.14408973252804141,Case 5: Sufficient coverage on both isoforms 4 | -------------------------------------------------------------------------------- /outrigger/tests/data/tasic2016/unprocessed/bam/CAV_LP_Ipsi_tdTpos_cell_1-SRR2140356-GSM1840944_R1.polyATrim.adapterTrim.rmRep.sorted.rg.subset.sorted.bam: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/YeoLab/outrigger/9da86d2d8d137b309a53cae8851ba867cf757201/outrigger/tests/data/tasic2016/unprocessed/bam/CAV_LP_Ipsi_tdTpos_cell_1-SRR2140356-GSM1840944_R1.polyATrim.adapterTrim.rmRep.sorted.rg.subset.sorted.bam -------------------------------------------------------------------------------- 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https://raw.githubusercontent.com/YeoLab/outrigger/9da86d2d8d137b309a53cae8851ba867cf757201/outrigger/tests/data/tasic2016/unprocessed/bam/CAV_LP_Ipsi_tdTpos_cell_2-SRR2140357-GSM1840945_R1.polyATrim.adapterTrim.rmRep.sorted.rg.subset.sorted.bam -------------------------------------------------------------------------------- /outrigger/tests/data/tasic2016/unprocessed/bam/CAV_LP_Ipsi_tdTpos_cell_2-SRR2140357-GSM1840945_R1.polyATrim.adapterTrim.rmRep.sorted.rg.subset.sorted.bam.bai: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/YeoLab/outrigger/9da86d2d8d137b309a53cae8851ba867cf757201/outrigger/tests/data/tasic2016/unprocessed/bam/CAV_LP_Ipsi_tdTpos_cell_2-SRR2140357-GSM1840945_R1.polyATrim.adapterTrim.rmRep.sorted.rg.subset.sorted.bam.bai -------------------------------------------------------------------------------- /outrigger/tests/data/tasic2016/unprocessed/gtf/gencode.vM10.annotation.snap25.myl6.gtf.db: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/YeoLab/outrigger/9da86d2d8d137b309a53cae8851ba867cf757201/outrigger/tests/data/tasic2016/unprocessed/gtf/gencode.vM10.annotation.snap25.myl6.gtf.db -------------------------------------------------------------------------------- /outrigger/tests/data/tasic2016/unprocessed/gtf/gencode.vM10.annotation.snap25.myl6.gtf.db.bak: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/YeoLab/outrigger/9da86d2d8d137b309a53cae8851ba867cf757201/outrigger/tests/data/tasic2016/unprocessed/gtf/gencode.vM10.annotation.snap25.myl6.gtf.db.bak -------------------------------------------------------------------------------- /outrigger/tests/data/tasic2016/unprocessed/gtf/gencode.vM10.annotation.subset.gtf.db: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/YeoLab/outrigger/9da86d2d8d137b309a53cae8851ba867cf757201/outrigger/tests/data/tasic2016/unprocessed/gtf/gencode.vM10.annotation.subset.gtf.db -------------------------------------------------------------------------------- /outrigger/tests/data/tasic2016/unprocessed/gtf/gencode.vM10.annotation.subset.with.novel.gtf.db: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/YeoLab/outrigger/9da86d2d8d137b309a53cae8851ba867cf757201/outrigger/tests/data/tasic2016/unprocessed/gtf/gencode.vM10.annotation.subset.with.novel.gtf.db -------------------------------------------------------------------------------- /outrigger/tests/data/tasic2016/unprocessed/samtools_filter_subset.sh: -------------------------------------------------------------------------------- 1 | #!/bin/bash 2 | 3 | PREFIX=CAV_LP_Ipsi_tdTpos_cell_1-SRR2140356-GSM1840944_R1.polyATrim.adapterTrim.rmRep.sorted.rg 4 | BAM1=$PREFIX.bam 5 | BAM2=$PREFIX.subset.bam 6 | samtools view -hb $BAM chr16:84827990-84834810 chr14:64123350-64417090 chr10:128491030-128502410 chr14:24490750-24495790 chr2:136713600-136781098 chr17:80201600-80207190 chr9:67024566-67043590 chr7:126487490-126490310 chr5:125386210-125389800 > $BAM2 7 | 8 | PREFIX3=$PREFIX.subset.sorted 9 | BAM3=$PREFIX3.bam 10 | samtools sort $BAM2 $PREFIX3 11 | 12 | samtools index $BAM3 13 | 14 | 15 | PREFIX=CAV_LP_Ipsi_tdTpos_cell_2-SRR2140357-GSM1840945_R1.polyATrim.adapterTrim.rmRep.sorted.rg 16 | -------------------------------------------------------------------------------- /outrigger/tests/data/tasic2016/unprocessed/sj_out_tab/Rbp4_tdTnegative_cell_19-SRR2139877-GSM1840465_R1.polyATrim.adapterTrim.rmRep.bamSJ.out.tab: -------------------------------------------------------------------------------- 1 | chr16 84821303 84822786 1 1 1 104 0 43 2 | chr16 84827996 84828424 2 2 1 105 7 47 3 | chr16 84828550 84831328 2 2 1 139 0 50 4 | chr10 128491034 128492058 2 2 1 14 184 49 5 | chr10 128492137 128492228 2 2 1 124 47 50 6 | chr14 24490759 24491749 1 1 1 18 70 30 7 | chr14 24491816 24491906 1 1 1 117 29 50 8 | chr14 24492117 24493382 1 1 1 351 3 50 9 | chr14 24493494 24495429 1 1 1 161 20 20 10 | chr14 24493494 24495774 1 1 1 62 3 49 11 | chr14 24495450 24495774 1 1 0 109 3 20 12 | chr5 125386215 125387354 2 2 0 0 1 37 13 | chr5 125386390 125387301 2 2 0 0 2 45 14 | chr5 125386443 125387354 2 2 0 0 1 26 15 | chr5 125386618 125387301 2 2 0 0 2 45 16 | chr5 125386618 125387529 2 2 0 0 145 46 17 | chr5 125386671 125387354 2 2 0 0 2 42 18 | chr5 125386846 125387301 2 2 0 0 2 45 19 | chr5 125386899 125387354 2 2 0 0 1 26 20 | chr5 125387074 125387301 2 2 0 0 2 45 21 | chr5 125387074 125387529 2 2 0 0 145 46 22 | chr5 125387127 125387354 2 2 0 0 2 42 23 | chr5 125387302 125387757 2 2 0 0 36 48 24 | chr5 125387302 125387985 2 2 0 0 65 48 25 | chr5 125387355 125387582 2 2 0 0 49 36 26 | chr5 125387355 125388038 2 2 0 0 49 36 27 | chr5 125387550 125388233 2 2 0 1 0 31 28 | chr5 125388265 125389696 2 2 1 119 0 48 29 | -------------------------------------------------------------------------------- /outrigger/tests/data/tasic2016/unprocessed/sj_out_tab/Rbp4_tdTnegative_cell_6-SRR2139864-GSM1840452_R1.polyATrim.adapterTrim.rmRep.bamSJ.out.tab: -------------------------------------------------------------------------------- 1 | chr16 84831508 84833993 2 2 1 1 0 11 2 | chr10 128492403 128492601 2 2 1 2 0 29 3 | chr14 24438951 24458042 1 1 0 0 2 17 4 | chr2 136713601 136756067 1 1 1 4 0 38 5 | chr2 136756202 136758310 1 1 1 4 0 42 6 | chr2 136758353 136763572 1 1 1 1 0 34 7 | chr2 136769861 136773894 1 1 1 1 1 16 8 | chr2 136770175 136773894 1 1 1 3 1 32 9 | chr2 136774021 136777335 1 1 1 5 0 40 10 | chr2 136777481 136781074 1 1 1 4 0 50 11 | chr17 80201603 80202168 2 2 1 118 0 36 12 | chr17 80202205 80202690 2 2 1 113 0 36 13 | chr17 80202745 80204130 2 2 0 96 0 49 14 | chr17 80204233 80204312 2 2 1 144 0 50 15 | chr17 80204388 80205261 2 2 1 122 0 48 16 | chr17 80205439 80205847 2 2 1 125 3 49 17 | chr17 80206029 80207174 2 2 1 146 0 50 18 | chr7 126489253 126489335 1 1 1 1 0 15 19 | chr5 125386390 125388213 2 2 0 0 1 31 20 | chr5 125386618 125387529 2 2 0 0 112 47 21 | chr5 125386618 125388213 2 2 0 0 1 31 22 | chr5 125386671 125387354 2 2 0 0 2 47 23 | chr5 125386846 125388213 2 2 0 0 1 31 24 | chr5 125387074 125387529 2 2 0 0 112 47 25 | chr5 125387074 125388213 2 2 0 0 1 31 26 | chr5 125387127 125387354 2 2 0 0 2 47 27 | chr5 125387302 125387757 2 2 0 0 40 48 28 | chr5 125387302 125387985 2 2 0 0 60 49 29 | chr5 125387355 125387582 2 2 0 0 70 37 30 | chr5 125387355 125388038 2 2 0 0 70 37 31 | chr5 125387530 125387757 2 2 0 1 0 25 32 | chr5 125387758 125388213 2 2 0 0 1 31 33 | chr5 125387986 125388213 2 2 0 0 1 31 34 | chr5 125388265 125389696 2 2 1 106 0 49 35 | -------------------------------------------------------------------------------- /outrigger/tests/data/tasic2016/unprocessed/sj_out_tab/Rbp4_tdTpositive_cell_174-SRR2139842-GSM1840430_R1.polyATrim.adapterTrim.rmRep.bamSJ.out.tab: -------------------------------------------------------------------------------- 1 | chr10 128492137 128492228 2 2 1 1 0 23 2 | chr10 128492403 128492601 2 2 1 3 0 41 3 | chr10 128492746 128493538 2 2 1 1 0 29 4 | chr14 24457100 24457218 2 2 1 1 0 38 5 | chr14 24484256 24484386 2 2 1 116 0 48 6 | chr14 24484523 24486872 2 2 1 71 0 48 7 | chr14 24490759 24491749 1 1 1 20 16 12 8 | chr14 24491816 24491906 1 1 1 43 2 44 9 | chr14 24492117 24493382 1 1 1 7 0 13 10 | chr2 136713601 136756067 1 1 1 131 6 50 11 | chr2 136756202 136758310 1 1 1 201 4 42 12 | chr2 136758353 136763572 1 1 1 212 4 43 13 | chr2 136763622 136769742 1 1 1 11 4 41 14 | chr2 136763622 136770056 1 1 1 131 4 50 15 | chr2 136769861 136773894 1 1 1 0 2 7 16 | chr2 136770175 136773894 1 1 1 71 2 49 17 | chr2 136774021 136777335 1 1 1 124 2 50 18 | chr2 136777481 136781074 1 1 1 117 0 50 19 | chr17 80206029 80207174 2 2 1 1 0 14 20 | chr7 126488755 126488836 1 1 1 1 0 36 21 | chr7 126489002 126489119 1 1 1 2 0 45 22 | chr7 126489253 126489335 1 1 1 2 0 20 23 | chr5 125386215 125387354 2 2 0 0 2 41 24 | chr5 125386443 125387354 2 2 0 0 2 41 25 | chr5 125386618 125387529 2 2 0 0 55 48 26 | chr5 125386899 125387354 2 2 0 0 2 41 27 | chr5 125387074 125387529 2 2 0 0 55 48 28 | chr5 125387302 125387757 2 2 0 0 15 43 29 | chr5 125387302 125387985 2 2 0 0 26 48 30 | chr5 125387355 125387582 2 2 0 0 15 48 31 | chr5 125387355 125387810 2 2 0 0 2 48 32 | chr5 125387355 125388038 2 2 0 0 15 48 33 | chr5 125387530 125387757 2 2 0 0 1 25 34 | chr5 125388265 125389696 2 2 1 5 0 39 35 | -------------------------------------------------------------------------------- /outrigger/tests/data/treutlein2014/intermediate/index/adjacencies/adjacent_junctions_single_exon.csv: -------------------------------------------------------------------------------- 1 | exon,direction,junction 2 | exon:chr7:130200983-130201173:-,upstream,junction:chr7:130196375-130200982:- 3 | exon:chr7:130200983-130201173:-,upstream,junction:chr7:130199906-130200982:- 4 | exon:chr7:130200983-130201173:-,downstream,junction:chr7:130201174-130218997:- 5 | -------------------------------------------------------------------------------- /outrigger/tests/data/treutlein2014/intermediate/index/adjacencies/single_junction_exon_triple.csv: -------------------------------------------------------------------------------- 1 | exon,direction,junction 2 | exon:chr7:130200983-130201173:-,downstream,junction:chr7:130201174-130218997:- 3 | -------------------------------------------------------------------------------- /outrigger/tests/data/treutlein2014/unprocessed/gtf/gencode.vM2.annotation.fgfr2.gtf.db: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/YeoLab/outrigger/9da86d2d8d137b309a53cae8851ba867cf757201/outrigger/tests/data/treutlein2014/unprocessed/gtf/gencode.vM2.annotation.fgfr2.gtf.db -------------------------------------------------------------------------------- /outrigger/tests/data/treutlein2014/unprocessed/sj_out_tab/SRR1033853_1.polyATrim.adapterTrim.rmRep.bamSJ.out.tab: -------------------------------------------------------------------------------- 1 | chr7 13032203 13032288 2 2 1 159 0 50 2 | chr7 13032351 13032434 2 2 1 141 0 50 3 | chr7 13034043 13034634 2 2 1 25 0 18 4 | chr7 130164216 130167702 2 2 1 7 0 45 5 | chr7 130167809 130169738 2 2 1 5 0 16 6 | chr7 130185381 130196177 2 2 1 57 0 50 7 | -------------------------------------------------------------------------------- /outrigger/tests/data/treutlein2014/unprocessed/sj_out_tab/SRR1033854_1.polyATrim.adapterTrim.rmRep.bamSJ.out.tab: -------------------------------------------------------------------------------- 1 | chr7 13015567 13016003 2 2 0 0 1 37 2 | chr7 13015811 13016003 2 2 0 0 1 42 3 | chr7 13032203 13032288 2 2 1 81 0 49 4 | chr7 13032351 13032434 2 2 1 97 0 49 5 | chr7 13032566 13032641 2 2 1 103 0 46 6 | chr7 13032822 13033828 2 2 1 76 0 49 7 | chr7 13034043 13034634 2 2 1 51 0 50 8 | chr7 130164124 130167702 2 2 1 33 2 46 9 | chr7 130164216 130167702 2 2 1 0 2 10 10 | chr7 130167809 130169738 2 2 1 28 0 49 11 | chr7 130169877 130171611 2 2 1 22 0 44 12 | chr7 130171683 130172816 2 2 1 5 0 40 13 | chr7 130172940 130177674 2 2 1 5 0 34 14 | chr7 130177866 130180364 2 2 1 4 0 43 15 | chr7 130180476 130182640 2 2 1 4 0 49 16 | chr7 130182763 130185228 2 2 1 4 0 26 17 | chr7 130185381 130196171 0 0 1 3 0 21 18 | chr7 130196375 130199757 2 2 1 10 0 47 19 | chr7 130199906 130200982 2 2 1 4 0 45 20 | chr7 130575140 130577213 1 1 0 16 0 50 21 | chr7 130742302 130751189 1 1 0 11 0 18 22 | chr7 130751334 130751833 1 1 1 27 0 45 23 | chr7 130751911 130753617 1 1 1 40 0 44 24 | chr7 130753662 130759164 1 1 1 38 0 44 25 | chr7 130897451 130900516 1 1 1 17 0 49 26 | chr7 130900661 130902176 1 1 1 7 0 47 27 | chr7 130902246 130904869 1 1 1 13 0 47 28 | chr7 130904935 130905390 1 1 1 11 0 40 29 | chr7 130905455 130908335 1 1 1 10 0 40 30 | chr7 130908426 130909587 1 1 1 11 0 42 31 | chr7 130909629 130910831 1 1 1 10 0 41 32 | chr7 130909736 130910831 1 1 1 1 0 3 33 | -------------------------------------------------------------------------------- /outrigger/tests/data/treutlein2014/unprocessed/sj_out_tab/SRR1033855_1.polyATrim.adapterTrim.rmRep.bamSJ.out.tab: -------------------------------------------------------------------------------- 1 | chr7 13034043 13034501 2 2 0 6 0 45 2 | -------------------------------------------------------------------------------- /outrigger/tests/data/treutlein2014/unprocessed/sj_out_tab/SRR1033856_1.polyATrim.adapterTrim.rmRep.bamSJ.out.tab: -------------------------------------------------------------------------------- 1 | chr7 13032203 13032288 2 2 1 16 0 50 2 | chr7 13032566 13032641 2 2 1 15 0 50 3 | chr7 13032822 13033828 2 2 1 12 0 48 4 | chr7 13034043 13034634 2 2 1 10 0 32 5 | -------------------------------------------------------------------------------- /outrigger/tests/data/treutlein2014/unprocessed/sj_out_tab/SRR1033857_1.polyATrim.adapterTrim.rmRep.bamSJ.out.tab: -------------------------------------------------------------------------------- 1 | chr7 130164124 130167702 2 2 1 4 1 49 2 | chr7 130164216 130167702 2 2 1 20 1 50 3 | chr7 130167809 130169738 2 2 1 38 0 48 4 | chr7 130169877 130171611 2 2 1 22 0 46 5 | chr7 130171683 130172816 2 2 1 22 0 47 6 | chr7 130172940 130177674 2 2 1 24 0 49 7 | chr7 130177866 130180364 2 2 1 18 1 48 8 | chr7 130180476 130182640 2 2 1 8 0 42 9 | chr7 130509259 130510810 2 2 1 71 0 50 10 | chr7 130510915 130513761 2 2 1 60 0 50 11 | chr7 130513825 130516104 2 2 1 98 0 50 12 | chr7 130516169 130519355 2 2 1 77 0 50 13 | -------------------------------------------------------------------------------- /outrigger/tests/data/treutlein2014/unprocessed/sj_out_tab/SRR1033858_1.polyATrim.adapterTrim.rmRep.bamSJ.out.tab: -------------------------------------------------------------------------------- 1 | chr7 13032203 13032288 2 2 1 7 0 30 2 | chr7 13032351 13032434 2 2 1 9 0 48 3 | chr7 13034043 13034634 2 2 1 52 0 50 4 | -------------------------------------------------------------------------------- /outrigger/tests/data/treutlein2014/unprocessed/sj_out_tab/SRR1033859_1.polyATrim.adapterTrim.rmRep.bamSJ.out.tab: -------------------------------------------------------------------------------- 1 | chr7 13032822 13033828 2 2 1 114 0 49 2 | chr7 13034043 13034634 2 2 1 104 0 50 3 | chr7 130593247 130596304 1 1 0 0 1 31 4 | -------------------------------------------------------------------------------- /outrigger/tests/data/treutlein2014/unprocessed/sj_out_tab/SRR1033860_1.polyATrim.adapterTrim.rmRep.bamSJ.out.tab: -------------------------------------------------------------------------------- 1 | chr7 13032203 13032288 2 2 1 213 0 50 2 | chr7 13032351 13032434 2 2 1 250 0 50 3 | chr7 13032566 13032641 2 2 1 309 0 49 4 | chr7 13032822 13033828 2 2 1 209 0 50 5 | chr7 13034043 13034634 2 2 1 147 0 50 6 | -------------------------------------------------------------------------------- /outrigger/tests/data/treutlein2014/unprocessed/sj_out_tab/SRR1033861_1.polyATrim.adapterTrim.rmRep.bamSJ.out.tab: -------------------------------------------------------------------------------- 1 | chr7 13032203 13032288 2 2 1 81 1 47 2 | chr7 13032351 13032434 2 2 1 43 0 48 3 | chr7 13032566 13032641 2 2 1 17 0 48 4 | chr7 13032822 13033828 2 2 1 26 0 45 5 | chr7 13034043 13034634 2 2 1 63 0 50 6 | -------------------------------------------------------------------------------- /outrigger/tests/data/treutlein2014/unprocessed/sj_out_tab/SRR1033862_1.polyATrim.adapterTrim.rmRep.bamSJ.out.tab: -------------------------------------------------------------------------------- 1 | chr7 13025062 13025303 1 1 1 7 0 47 2 | chr7 13025417 13025643 1 1 1 19 0 47 3 | chr7 13025777 13027616 1 1 1 19 0 50 4 | chr7 13032203 13032288 2 2 1 253 0 50 5 | chr7 13032351 13032434 2 2 1 292 0 50 6 | chr7 13032566 13032641 2 2 1 329 0 50 7 | chr7 13032822 13033828 2 2 1 244 0 50 8 | chr7 13034043 13034634 2 2 1 208 0 50 9 | -------------------------------------------------------------------------------- /outrigger/tests/data/treutlein2014/unprocessed/sj_out_tab/SRR1033863_1.polyATrim.adapterTrim.rmRep.bamSJ.out.tab: -------------------------------------------------------------------------------- 1 | chr7 13030207 13030288 1 1 1 267 0 50 2 | chr7 13030376 13030454 1 1 1 253 0 50 3 | chr7 13030593 13030688 1 1 1 295 0 50 4 | -------------------------------------------------------------------------------- /outrigger/tests/data/treutlein2014/unprocessed/sj_out_tab/SRR1033864_1.polyATrim.adapterTrim.rmRep.bamSJ.out.tab: -------------------------------------------------------------------------------- 1 | chr7 130164124 130167702 2 2 1 82 13 49 2 | chr7 130164216 130167702 2 2 1 0 13 11 3 | -------------------------------------------------------------------------------- /outrigger/tests/data/treutlein2014/unprocessed/sj_out_tab/SRR1033865_1.polyATrim.adapterTrim.rmRep.bamSJ.out.tab: -------------------------------------------------------------------------------- 1 | chr7 13032203 13032288 2 2 1 10 0 50 2 | chr7 13032351 13032434 2 2 1 12 0 39 3 | chr7 13032566 13032641 2 2 1 9 0 45 4 | chr7 13032822 13033828 2 2 1 5 0 39 5 | chr7 13034043 13034634 2 2 1 2 0 19 6 | -------------------------------------------------------------------------------- /outrigger/tests/data/treutlein2014/unprocessed/sj_out_tab/SRR1033866_1.polyATrim.adapterTrim.rmRep.bamSJ.out.tab: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/YeoLab/outrigger/9da86d2d8d137b309a53cae8851ba867cf757201/outrigger/tests/data/treutlein2014/unprocessed/sj_out_tab/SRR1033866_1.polyATrim.adapterTrim.rmRep.bamSJ.out.tab -------------------------------------------------------------------------------- /outrigger/tests/data/treutlein2014/unprocessed/sj_out_tab/SRR1033867_1.polyATrim.adapterTrim.rmRep.bamSJ.out.tab: -------------------------------------------------------------------------------- 1 | chr7 13030593 13030688 1 1 1 1 0 39 2 | chr7 13032203 13032288 2 2 1 270 0 50 3 | chr7 13032351 13032434 2 2 1 347 0 50 4 | chr7 13032566 13032641 2 2 1 386 0 50 5 | chr7 13032822 13033828 2 2 1 347 0 50 6 | chr7 13034043 13034634 2 2 1 246 0 50 7 | -------------------------------------------------------------------------------- /outrigger/tests/data/treutlein2014/unprocessed/sj_out_tab/SRR1033868_1.polyATrim.adapterTrim.rmRep.bamSJ.out.tab: -------------------------------------------------------------------------------- 1 | chr7 13030593 13030688 1 1 1 2 0 19 2 | chr7 13032203 13032288 2 2 1 217 0 50 3 | chr7 13032351 13032434 2 2 1 271 0 50 4 | chr7 13032566 13032641 2 2 1 308 0 49 5 | chr7 13032822 13033828 2 2 1 215 0 50 6 | chr7 13034043 13034634 2 2 1 240 0 50 7 | chr7 130509259 130510810 2 2 1 90 7 50 8 | chr7 130510915 130513761 2 2 1 80 4 50 9 | chr7 130513825 130516104 2 2 1 122 3 50 10 | chr7 130516169 130519876 2 2 1 99 0 19 11 | -------------------------------------------------------------------------------- /outrigger/tests/data/treutlein2014/unprocessed/sj_out_tab/SRR1033869_1.polyATrim.adapterTrim.rmRep.bamSJ.out.tab: -------------------------------------------------------------------------------- 1 | chr7 13030593 13030688 1 1 1 1 0 39 2 | chr7 130667740 130667762 1 1 0 1 0 39 3 | -------------------------------------------------------------------------------- /outrigger/tests/data/treutlein2014/unprocessed/sj_out_tab/SRR1033870_1.polyATrim.adapterTrim.rmRep.bamSJ.out.tab: -------------------------------------------------------------------------------- 1 | chr7 13030593 13030688 1 1 1 2 0 38 2 | chr7 130509259 130510810 2 2 1 2 0 44 3 | chr7 130510915 130513761 2 2 1 2 0 15 4 | -------------------------------------------------------------------------------- /outrigger/tests/data/treutlein2014/unprocessed/sj_out_tab/SRR1033871_1.polyATrim.adapterTrim.rmRep.bamSJ.out.tab: -------------------------------------------------------------------------------- 1 | chr7 13030593 13030688 1 1 1 2 0 39 2 | chr7 13032203 13032288 2 2 1 423 0 50 3 | chr7 13032351 13032434 2 2 1 492 0 50 4 | chr7 13032566 13032641 2 2 1 605 0 50 5 | chr7 13032822 13033828 2 2 1 607 0 50 6 | chr7 13034043 13034634 2 2 1 503 0 50 7 | chr7 130510915 130513761 2 2 1 3 0 23 8 | chr7 130513825 130516104 2 2 1 1 0 36 9 | chr7 130729829 130733505 1 1 0 6 0 39 10 | chr7 130733567 130734948 1 1 1 8 0 49 11 | chr7 130735151 130739811 1 1 1 14 0 47 12 | chr7 130739874 130740839 1 1 1 15 0 50 13 | chr7 130740956 130742129 1 1 1 8 0 36 14 | chr7 130742302 130751189 1 1 0 10 0 50 15 | chr7 130751334 130751833 1 1 1 3 0 44 16 | chr7 130751911 130753617 1 1 1 11 0 44 17 | chr7 130753662 130759164 1 1 1 5 0 44 18 | -------------------------------------------------------------------------------- /outrigger/tests/data/treutlein2014/unprocessed/sj_out_tab/SRR1033872_1.polyATrim.adapterTrim.rmRep.bamSJ.out.tab: -------------------------------------------------------------------------------- 1 | chr7 13029257 13068909 1 1 0 1 0 12 2 | chr7 13032203 13032288 2 2 1 246 0 50 3 | chr7 13032351 13032434 2 2 1 266 0 50 4 | chr7 13032566 13032641 2 2 1 281 0 50 5 | chr7 13032822 13033828 2 2 1 178 0 50 6 | chr7 13034043 13034634 2 2 1 140 0 49 7 | chr7 130759326 130759533 1 1 1 73 0 38 8 | chr7 130759641 130759914 1 1 1 126 0 50 9 | chr7 130760036 130764253 1 1 1 117 0 50 10 | -------------------------------------------------------------------------------- /outrigger/tests/data/treutlein2014/unprocessed/sj_out_tab/SRR1033873_1.polyATrim.adapterTrim.rmRep.bamSJ.out.tab: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/YeoLab/outrigger/9da86d2d8d137b309a53cae8851ba867cf757201/outrigger/tests/data/treutlein2014/unprocessed/sj_out_tab/SRR1033873_1.polyATrim.adapterTrim.rmRep.bamSJ.out.tab -------------------------------------------------------------------------------- /outrigger/tests/data/treutlein2014/unprocessed/sj_out_tab/SRR1033874_1.polyATrim.adapterTrim.rmRep.bamSJ.out.tab: -------------------------------------------------------------------------------- 1 | chr7 13028988 13029087 1 1 1 1 0 45 2 | chr7 13029596 13029675 1 1 1 1 0 23 3 | chr7 13029996 13030082 1 1 1 7 0 34 4 | chr7 13030207 13030288 1 1 1 8 0 35 5 | chr7 13030376 13030454 1 1 1 6 0 45 6 | chr7 13030593 13030688 1 1 1 1 0 37 7 | chr7 13032203 13032288 2 2 1 45 0 50 8 | chr7 13032351 13032434 2 2 1 29 0 50 9 | chr7 13032566 13032641 2 2 1 25 0 45 10 | chr7 13032822 13033828 2 2 1 19 0 49 11 | chr7 13034043 13034501 2 2 0 5 0 42 12 | chr7 13034043 13034634 2 2 1 35 0 50 13 | chr7 130164124 130167702 2 2 1 4 1 29 14 | chr7 130164216 130167702 2 2 1 0 1 9 15 | chr7 130167809 130169738 2 2 1 5 0 50 16 | chr7 130169877 130171611 2 2 1 1 0 13 17 | chr7 130171683 130172816 2 2 1 2 0 33 18 | chr7 130177866 130180364 2 2 1 1 0 43 19 | chr7 130180476 130182640 2 2 1 2 0 32 20 | chr7 130185381 130196171 0 0 1 1 0 46 21 | chr7 130196375 130199757 2 2 1 1 0 28 22 | chr7 130201174 130218997 2 2 1 1 0 29 23 | chr7 130394737 130418447 2 2 1 2 0 43 24 | chr7 130464231 130467255 2 2 1 1 0 31 25 | chr7 130481716 130504693 2 2 1 1 0 7 26 | chr7 130516169 130519876 2 2 1 1 0 22 27 | chr7 130532693 130533576 2 2 1 2 0 46 28 | chr7 130533862 130535523 2 2 1 1 0 11 29 | chr7 130537078 130538161 2 2 1 2 0 39 30 | chr7 130739874 130740839 1 1 1 1 0 41 31 | chr7 130740956 130742129 1 1 1 2 0 33 32 | chr7 130742302 130751189 1 1 0 2 0 44 33 | chr7 130751334 130751833 1 1 1 1 0 37 34 | chr7 130751911 130753617 1 1 1 2 0 44 35 | chr7 130759326 130759533 1 1 1 1 0 34 36 | chr7 130759641 130759914 1 1 1 5 0 45 37 | chr7 130760036 130764253 1 1 1 3 0 19 38 | -------------------------------------------------------------------------------- /outrigger/tests/data/treutlein2014/unprocessed/sj_out_tab/SRR1033875_1.polyATrim.adapterTrim.rmRep.bamSJ.out.tab: -------------------------------------------------------------------------------- 1 | chr7 130510915 130513761 2 2 1 1 0 11 2 | chr7 130866692 130877733 1 1 0 1 0 45 3 | chr7 130877895 130882329 1 1 1 1 0 22 4 | chr7 130882387 130885402 1 1 1 1 0 19 5 | -------------------------------------------------------------------------------- /outrigger/tests/data/treutlein2014/unprocessed/sj_out_tab/SRR1033876_1.polyATrim.adapterTrim.rmRep.bamSJ.out.tab: -------------------------------------------------------------------------------- 1 | chr7 130645622 130645842 2 2 0 2 0 48 2 | chr7 130716840 130728522 1 1 1 0 1 3 3 | chr7 130716978 130728522 1 1 0 4 0 19 4 | chr7 130877895 130882329 1 1 1 1 0 30 5 | -------------------------------------------------------------------------------- /outrigger/tests/data/treutlein2014/unprocessed/sj_out_tab/SRR1033877_1.polyATrim.adapterTrim.rmRep.bamSJ.out.tab: -------------------------------------------------------------------------------- 1 | chr7 130532693 130533576 2 2 1 26 0 49 2 | chr7 130533667 130533769 2 2 1 22 1 27 3 | chr7 130866692 130877733 1 1 0 2 0 31 4 | chr7 130877895 130882329 1 1 1 2 0 26 5 | chr7 130882387 130885402 1 1 1 1 0 8 6 | chr7 130892279 130897324 1 1 1 1 0 10 7 | -------------------------------------------------------------------------------- /outrigger/tests/data/treutlein2014/unprocessed/sj_out_tab/SRR1033878_1.polyATrim.adapterTrim.rmRep.bamSJ.out.tab: -------------------------------------------------------------------------------- 1 | chr7 13032203 13032288 2 2 1 8 0 43 2 | chr7 13032351 13032434 2 2 1 5 0 38 3 | chr7 13032566 13032641 2 2 1 7 0 49 4 | chr7 13032822 13033828 2 2 1 3 0 32 5 | chr7 13034043 13034634 2 2 1 4 0 47 6 | chr7 130164124 130167702 2 2 1 23 2 46 7 | chr7 130164216 130167702 2 2 1 0 2 9 8 | chr7 130167809 130169738 2 2 1 19 0 50 9 | chr7 130169877 130171611 2 2 1 20 0 48 10 | chr7 130171683 130172816 2 2 1 27 0 46 11 | chr7 130172940 130177674 2 2 1 14 0 48 12 | chr7 130177866 130180364 2 2 1 8 0 6 13 | chr7 130866692 130877733 1 1 0 1 0 21 14 | chr7 130885449 130892180 1 1 1 1 0 39 15 | -------------------------------------------------------------------------------- /outrigger/tests/data/treutlein2014/unprocessed/sj_out_tab/SRR1033879_1.polyATrim.adapterTrim.rmRep.bamSJ.out.tab: -------------------------------------------------------------------------------- 1 | chr7 13032351 13032434 2 2 1 26 0 43 2 | chr7 130751334 130751833 1 1 1 25 0 44 3 | chr7 130751911 130753617 1 1 1 30 0 44 4 | chr7 130753662 130759164 1 1 1 26 0 45 5 | chr7 130759326 130759533 1 1 1 19 0 49 6 | chr7 130759641 130759914 1 1 1 83 0 49 7 | chr7 130760036 130764253 1 1 1 85 0 50 8 | chr7 130877895 130882329 1 1 1 1 0 19 9 | chr7 130882387 130885402 1 1 1 2 0 25 10 | chr7 130885449 130892180 1 1 1 2 0 45 11 | -------------------------------------------------------------------------------- /outrigger/tests/data/treutlein2014/unprocessed/sj_out_tab/SRR1033880_1.polyATrim.adapterTrim.rmRep.bamSJ.out.tab: -------------------------------------------------------------------------------- 1 | chr7 13032203 13032288 2 2 1 53 0 50 2 | chr7 13032351 13032434 2 2 1 67 0 48 3 | chr7 13032566 13032641 2 2 1 56 0 49 4 | chr7 13032822 13033828 2 2 1 37 0 45 5 | chr7 13034043 13034634 2 2 1 28 0 50 6 | chr7 130532084 130533576 2 2 0 3 0 32 7 | chr7 130533862 130536982 2 2 0 8 0 49 8 | chr7 130537078 130538161 2 2 1 4 0 41 9 | chr7 130538253 130539010 2 2 1 5 0 50 10 | chr7 130539111 130539813 2 2 1 5 0 42 11 | chr7 130539966 130546991 2 2 0 6 0 44 12 | -------------------------------------------------------------------------------- /outrigger/tests/data/treutlein2014/unprocessed/sj_out_tab/SRR1033881_1.polyATrim.adapterTrim.rmRep.bamSJ.out.tab: -------------------------------------------------------------------------------- 1 | chr7 13032203 13032288 2 2 1 1 0 34 2 | chr7 13032351 13032434 2 2 1 5 0 48 3 | chr7 13032566 13032641 2 2 1 6 0 45 4 | chr7 13032822 13033828 2 2 1 2 0 41 5 | chr7 13034043 13034501 2 2 0 2 0 49 6 | chr7 130877895 130882329 1 1 1 4 0 40 7 | chr7 130882387 130885402 1 1 1 4 0 28 8 | chr7 130885449 130892180 1 1 1 4 0 45 9 | chr7 130892279 130897324 1 1 1 1 0 39 10 | -------------------------------------------------------------------------------- /outrigger/tests/data/treutlein2014/unprocessed/sj_out_tab/SRR1033882_1.polyATrim.adapterTrim.rmRep.bamSJ.out.tab: -------------------------------------------------------------------------------- 1 | chr7 13032203 13032288 2 2 1 6 0 50 2 | chr7 13032351 13032434 2 2 1 5 0 38 3 | chr7 13032566 13032641 2 2 1 5 0 45 4 | chr7 13032822 13033828 2 2 1 8 0 42 5 | chr7 13034043 13034634 2 2 1 4 0 49 6 | chr7 130866692 130877733 1 1 0 6 0 45 7 | chr7 130877895 130882329 1 1 1 2 0 25 8 | chr7 130882387 130885402 1 1 1 4 0 46 9 | chr7 130885449 130892180 1 1 1 2 0 28 10 | -------------------------------------------------------------------------------- /outrigger/tests/data/treutlein2014/unprocessed/sj_out_tab/SRR1033883_1.polyATrim.adapterTrim.rmRep.bamSJ.out.tab: -------------------------------------------------------------------------------- 1 | chr7 13032203 13032288 2 2 1 225 0 50 2 | chr7 13032351 13032434 2 2 1 218 0 50 3 | chr7 13032566 13032641 2 2 1 182 0 49 4 | chr7 13032822 13033828 2 2 1 124 2 49 5 | chr7 13034039 13034630 2 2 0 1 0 28 6 | chr7 13034043 13034634 2 2 1 72 1 49 7 | chr7 130866692 130877733 1 1 0 1 0 21 8 | chr7 130877895 130882329 1 1 1 2 0 19 9 | chr7 130882387 130885402 1 1 1 5 0 34 10 | chr7 130885449 130892180 1 1 1 4 0 46 11 | chr7 130892279 130897324 1 1 1 4 0 37 12 | -------------------------------------------------------------------------------- /outrigger/tests/data/treutlein2014/unprocessed/sj_out_tab/SRR1033884_1.polyATrim.adapterTrim.rmRep.bamSJ.out.tab: -------------------------------------------------------------------------------- 1 | chr7 13032203 13032288 2 2 1 102 0 50 2 | chr7 13032351 13032434 2 2 1 126 0 50 3 | chr7 13032566 13032641 2 2 1 149 0 50 4 | chr7 13032822 13033828 2 2 1 95 0 50 5 | chr7 13034043 13034634 2 2 1 58 0 49 6 | chr7 130509259 130510810 2 2 1 34 0 48 7 | chr7 130510915 130513761 2 2 1 44 1 48 8 | chr7 130513825 130516104 2 2 1 64 0 50 9 | chr7 130516169 130519876 2 2 1 37 0 50 10 | chr7 130532693 130533576 2 2 1 41 0 50 11 | chr7 130533667 130533769 2 2 1 28 0 25 12 | chr7 130644589 130645467 2 2 0 1 0 27 13 | chr7 130877895 130882329 1 1 1 2 0 29 14 | chr7 130882387 130885402 1 1 1 2 0 20 15 | chr7 130885449 130892180 1 1 1 1 0 35 16 | chr7 130892279 130897324 1 1 1 1 0 38 17 | -------------------------------------------------------------------------------- /outrigger/tests/data/treutlein2014/unprocessed/sj_out_tab/SRR1033885_1.polyATrim.adapterTrim.rmRep.bamSJ.out.tab: -------------------------------------------------------------------------------- 1 | chr7 13032203 13032288 2 2 1 17 0 46 2 | chr7 13032351 13032434 2 2 1 15 0 50 3 | chr7 13032566 13032641 2 2 1 12 0 44 4 | chr7 13032822 13033828 2 2 1 9 0 46 5 | chr7 13034043 13034634 2 2 1 7 0 45 6 | chr7 130219122 130228622 2 2 1 3 0 14 7 | chr7 130228793 130241199 2 2 1 6 0 34 8 | chr7 130241278 130242377 2 2 1 6 0 50 9 | chr7 130759641 130759914 1 1 1 13 0 46 10 | chr7 130760036 130764253 1 1 1 13 1 50 11 | chr7 130866692 130877733 1 1 0 2 0 32 12 | chr7 130877895 130882329 1 1 1 3 0 19 13 | chr7 130882387 130885402 1 1 1 3 0 46 14 | chr7 130885449 130892180 1 1 1 4 0 20 15 | chr7 130892279 130897324 1 1 1 18 0 48 16 | chr7 130897451 130900516 1 1 1 22 0 49 17 | chr7 130900661 130902176 1 1 1 28 0 50 18 | chr7 130902246 130904869 1 1 1 26 0 47 19 | chr7 130904935 130905390 1 1 1 25 0 48 20 | chr7 130905455 130908335 1 1 1 35 0 50 21 | chr7 130908426 130909587 1 1 1 26 0 41 22 | chr7 130909629 130910831 1 1 1 29 0 41 23 | chr7 130936744 130961512 1 1 1 5 0 43 24 | chr7 130961613 130961972 1 1 1 12 0 49 25 | chr7 130962178 130979300 1 1 1 10 0 47 26 | chr7 130979496 130979951 1 1 1 5 0 33 27 | chr7 130979985 130981656 1 1 1 7 0 33 28 | chr7 130981772 130982236 1 1 1 5 0 45 29 | chr7 130982295 130983659 1 1 1 7 0 49 30 | chr7 130983756 130984962 1 1 1 9 0 48 31 | -------------------------------------------------------------------------------- /outrigger/tests/data/treutlein2014/unprocessed/sj_out_tab/SRR1033886_1.polyATrim.adapterTrim.rmRep.bamSJ.out.tab: -------------------------------------------------------------------------------- 1 | chr7 13029996 13030082 1 1 1 4 0 3 2 | chr7 13030207 13030288 1 1 1 23 0 50 3 | chr7 13030376 13030454 1 1 1 34 0 47 4 | chr7 13030593 13030688 1 1 1 26 0 45 5 | chr7 13034043 13034634 2 2 1 18 0 49 6 | chr7 130164124 130167702 2 2 1 4 7 47 7 | chr7 130164216 130167702 2 2 1 55 7 50 8 | chr7 130167809 130169738 2 2 1 70 1 50 9 | chr7 130169877 130171611 2 2 1 81 0 50 10 | chr7 130171683 130172816 2 2 1 66 0 49 11 | chr7 130172940 130177674 2 2 1 42 0 49 12 | chr7 130177866 130180364 2 2 1 53 0 46 13 | chr7 130180476 130182640 2 2 1 40 0 47 14 | chr7 130345214 130351657 0 0 1 0 1 44 15 | chr7 130742302 130751189 1 1 0 10 0 45 16 | chr7 130751334 130751833 1 1 1 10 0 38 17 | chr7 130751911 130753617 1 1 1 14 0 44 18 | chr7 130753662 130759164 1 1 1 13 0 44 19 | chr7 130759326 130759533 1 1 1 15 0 42 20 | chr7 130759641 130759914 1 1 1 12 0 47 21 | chr7 130760036 130764253 1 1 1 11 0 45 22 | chr7 130866692 130877733 1 1 0 2 0 45 23 | chr7 130982782 130983659 1 1 1 38 0 49 24 | chr7 130983756 130984962 1 1 1 58 0 50 25 | -------------------------------------------------------------------------------- /outrigger/tests/data/treutlein2014/unprocessed/sj_out_tab/SRR1033887_1.polyATrim.adapterTrim.rmRep.bamSJ.out.tab: -------------------------------------------------------------------------------- 1 | chr7 130866692 130877733 1 1 0 3 0 50 2 | chr7 130877895 130882329 1 1 1 3 0 39 3 | chr7 130882387 130885402 1 1 1 4 0 46 4 | chr7 130885449 130892180 1 1 1 3 0 46 5 | -------------------------------------------------------------------------------- /outrigger/tests/data/treutlein2014/unprocessed/sj_out_tab/SRR1033888_1.polyATrim.adapterTrim.rmRep.bamSJ.out.tab: -------------------------------------------------------------------------------- 1 | chr7 13032203 13032288 2 2 1 102 0 49 2 | chr7 13032351 13032434 2 2 1 92 0 50 3 | chr7 130866692 130877733 1 1 0 3 0 49 4 | chr7 130877895 130882329 1 1 1 4 0 47 5 | chr7 130882387 130885402 1 1 1 1 0 37 6 | chr7 130885449 130892180 1 1 1 1 0 9 7 | chr7 130892279 130897324 1 1 1 2 0 28 8 | -------------------------------------------------------------------------------- /outrigger/tests/data/treutlein2014/unprocessed/sj_out_tab/SRR1033889_1.polyATrim.adapterTrim.rmRep.bamSJ.out.tab: -------------------------------------------------------------------------------- 1 | chr7 13032203 13032288 2 2 1 24 0 48 2 | chr7 13032351 13032434 2 2 1 27 0 48 3 | chr7 13032566 13032641 2 2 1 34 0 45 4 | chr7 13032822 13033828 2 2 1 18 0 39 5 | chr7 13034043 13034634 2 2 1 1 0 25 6 | chr7 130509259 130510810 2 2 1 29 0 36 7 | chr7 130510915 130513761 2 2 1 28 0 48 8 | chr7 130513825 130516104 2 2 1 43 0 50 9 | chr7 130516169 130519355 2 2 1 25 0 50 10 | chr7 130740956 130742129 1 1 1 68 1 37 11 | chr7 130742302 130751189 1 1 0 67 0 50 12 | chr7 130751334 130751833 1 1 1 117 0 50 13 | chr7 130751911 130753617 1 1 1 112 0 44 14 | chr7 130753662 130759164 1 1 1 106 0 46 15 | chr7 130759326 130759533 1 1 1 142 0 50 16 | chr7 130759641 130759914 1 1 1 125 0 50 17 | chr7 130760036 130764253 1 1 1 98 0 50 18 | chr7 130866692 130877733 1 1 0 1 0 22 19 | chr7 130877895 130882329 1 1 1 1 0 19 20 | chr7 130882387 130885402 1 1 1 1 0 17 21 | chr7 130885449 130892180 1 1 1 1 0 38 22 | chr7 130892279 130897324 1 1 1 2 0 19 23 | -------------------------------------------------------------------------------- /outrigger/tests/data/treutlein2014/unprocessed/sj_out_tab/SRR1033890_1.polyATrim.adapterTrim.rmRep.bamSJ.out.tab: -------------------------------------------------------------------------------- 1 | chr7 13030593 13030688 1 1 1 2 0 29 2 | chr7 13032203 13032288 2 2 1 64 0 50 3 | chr7 13032351 13032434 2 2 1 56 0 48 4 | chr7 13032566 13032641 2 2 1 28 0 50 5 | chr7 13032822 13033828 2 2 1 10 0 47 6 | chr7 13034043 13034634 2 2 1 13 0 49 7 | chr7 130164124 130167702 2 2 1 30 2 46 8 | chr7 130164216 130167702 2 2 1 0 2 10 9 | chr7 130866001 130877733 1 1 1 15 0 44 10 | chr7 130877895 130882329 1 1 1 30 0 48 11 | chr7 130882387 130885402 1 1 1 31 0 48 12 | chr7 130885449 130892180 1 1 1 29 0 48 13 | chr7 130892279 130897324 1 1 1 10 0 48 14 | chr7 130897451 130900516 1 1 1 15 0 50 15 | chr7 130900661 130902176 1 1 1 22 0 47 16 | chr7 130902246 130905390 1 1 0 14 0 46 17 | chr7 130905455 130908335 1 1 1 18 0 50 18 | chr7 130908426 130909587 1 1 1 31 0 50 19 | chr7 130909736 130910831 1 1 1 27 0 49 20 | chr7 130962178 130979300 1 1 1 0 1 3 21 | -------------------------------------------------------------------------------- /outrigger/tests/data/treutlein2014/unprocessed/sj_out_tab/SRR1033891_1.polyATrim.adapterTrim.rmRep.bamSJ.out.tab: -------------------------------------------------------------------------------- 1 | chr7 13032203 13032288 2 2 1 46 1 50 2 | chr7 13032351 13032434 2 2 1 57 1 50 3 | chr7 13032566 13032641 2 2 1 58 1 49 4 | chr7 13032822 13033828 2 2 1 30 0 49 5 | chr7 13034043 13034634 2 2 1 27 0 50 6 | chr7 130532693 130533576 2 2 1 5 0 21 7 | chr7 130882387 130885402 1 1 1 1 0 8 8 | chr7 130885449 130892180 1 1 1 1 0 46 9 | -------------------------------------------------------------------------------- /outrigger/tests/data/treutlein2014/unprocessed/sj_out_tab/SRR1033892_1.polyATrim.adapterTrim.rmRep.bamSJ.out.tab: -------------------------------------------------------------------------------- 1 | chr7 13032203 13032288 2 2 1 3 0 36 2 | chr7 13032351 13032434 2 2 1 5 0 46 3 | chr7 130532693 130533576 2 2 1 38 0 47 4 | chr7 130877895 130882329 1 1 1 35 0 50 5 | chr7 130882387 130885402 1 1 1 34 0 49 6 | chr7 130885449 130892180 1 1 1 38 0 48 7 | chr7 130892279 130897324 1 1 1 24 0 45 8 | -------------------------------------------------------------------------------- /outrigger/tests/data/treutlein2014/unprocessed/sj_out_tab/SRR1033893_1.polyATrim.adapterTrim.rmRep.bamSJ.out.tab: -------------------------------------------------------------------------------- 1 | chr7 13032203 13032288 2 2 1 80 0 49 2 | chr7 13032351 13032434 2 2 1 79 0 50 3 | chr7 13032566 13032641 2 2 1 72 0 46 4 | chr7 13032822 13033828 2 2 1 55 0 50 5 | chr7 13034039 13034630 2 2 0 1 0 26 6 | chr7 13034043 13034634 2 2 1 47 0 49 7 | chr7 130509259 130510810 2 2 1 120 0 50 8 | chr7 130510915 130513761 2 2 1 117 0 50 9 | chr7 130513825 130516104 2 2 1 166 0 50 10 | chr7 130516169 130519355 2 2 1 107 0 50 11 | chr7 130516169 130519876 2 2 1 101 0 50 12 | -------------------------------------------------------------------------------- /outrigger/tests/data/treutlein2014/unprocessed/sj_out_tab/SRR1033894_1.polyATrim.adapterTrim.rmRep.bamSJ.out.tab: -------------------------------------------------------------------------------- 1 | chr7 13028993 13030665 2 2 0 4 0 45 2 | -------------------------------------------------------------------------------- /outrigger/tests/data/treutlein2014/unprocessed/sj_out_tab/SRR1033895_1.polyATrim.adapterTrim.rmRep.bamSJ.out.tab: -------------------------------------------------------------------------------- 1 | chr7 13030207 13030288 1 1 1 3 0 9 2 | chr7 13030376 13030454 1 1 1 25 0 50 3 | chr7 13030593 13030688 1 1 1 33 0 49 4 | chr7 13032203 13032288 2 2 1 48 0 50 5 | chr7 13032351 13032434 2 2 1 52 0 48 6 | chr7 13032566 13032641 2 2 1 39 0 46 7 | chr7 13032822 13033828 2 2 1 20 0 47 8 | chr7 13034043 13034634 2 2 1 12 0 32 9 | -------------------------------------------------------------------------------- /outrigger/tests/data/treutlein2014/unprocessed/sj_out_tab/SRR1033896_1.polyATrim.adapterTrim.rmRep.bamSJ.out.tab: -------------------------------------------------------------------------------- 1 | chr7 130626842 130663015 1 1 1 2 1 3 2 | chr7 130663142 130674601 1 1 1 2 0 16 3 | -------------------------------------------------------------------------------- /outrigger/tests/data/treutlein2014/unprocessed/sj_out_tab/SRR1033897_1.polyATrim.adapterTrim.rmRep.bamSJ.out.tab: -------------------------------------------------------------------------------- 1 | chr7 13030376 13030454 1 1 1 162 0 50 2 | chr7 13030593 13030688 1 1 1 205 0 49 3 | chr7 130183322 130185228 2 2 0 1 0 17 4 | chr7 130533862 130535523 2 2 1 1 0 18 5 | chr7 130535573 130536982 2 2 1 1 0 9 6 | chr7 130882387 130885402 1 1 1 17 0 19 7 | chr7 130885449 130892180 1 1 1 27 0 48 8 | chr7 130892279 130897324 1 1 1 15 0 42 9 | -------------------------------------------------------------------------------- /outrigger/tests/data/treutlein2014/unprocessed/sj_out_tab/SRR1033898_1.polyATrim.adapterTrim.rmRep.bamSJ.out.tab: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/YeoLab/outrigger/9da86d2d8d137b309a53cae8851ba867cf757201/outrigger/tests/data/treutlein2014/unprocessed/sj_out_tab/SRR1033898_1.polyATrim.adapterTrim.rmRep.bamSJ.out.tab -------------------------------------------------------------------------------- /outrigger/tests/data/treutlein2014/unprocessed/sj_out_tab/SRR1033899_1.polyATrim.adapterTrim.rmRep.bamSJ.out.tab: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/YeoLab/outrigger/9da86d2d8d137b309a53cae8851ba867cf757201/outrigger/tests/data/treutlein2014/unprocessed/sj_out_tab/SRR1033899_1.polyATrim.adapterTrim.rmRep.bamSJ.out.tab -------------------------------------------------------------------------------- /outrigger/tests/data/treutlein2014/unprocessed/sj_out_tab/SRR1033900_1.polyATrim.adapterTrim.rmRep.bamSJ.out.tab: -------------------------------------------------------------------------------- 1 | chr7 130394737 130418447 2 2 1 5 2 42 2 | chr7 130509259 130510810 2 2 1 139 0 50 3 | chr7 130510915 130513761 2 2 1 139 1 50 4 | chr7 130513825 130516104 2 2 1 171 0 50 5 | chr7 130516169 130519355 2 2 1 98 0 50 6 | -------------------------------------------------------------------------------- /outrigger/tests/data/treutlein2014/unprocessed/sj_out_tab/SRR1033901_1.polyATrim.adapterTrim.rmRep.bamSJ.out.tab: -------------------------------------------------------------------------------- 1 | chr7 13032203 13032288 2 2 1 97 0 50 2 | chr7 13032351 13032434 2 2 1 109 0 50 3 | chr7 13032566 13032641 2 2 1 110 0 49 4 | chr7 13032822 13033828 2 2 1 65 0 49 5 | chr7 13034043 13034634 2 2 1 46 0 49 6 | chr7 130394737 130418447 2 2 1 45 0 49 7 | chr7 130418569 130464130 2 2 1 58 0 49 8 | chr7 130464231 130467255 2 2 1 41 0 50 9 | chr7 130467438 130481682 2 2 1 31 0 36 10 | chr7 130481716 130504693 2 2 1 21 0 34 11 | -------------------------------------------------------------------------------- /outrigger/tests/data/treutlein2014/unprocessed/sj_out_tab/SRR1033902_1.polyATrim.adapterTrim.rmRep.bamSJ.out.tab: -------------------------------------------------------------------------------- 1 | chr7 13032203 13032288 2 2 1 35 0 50 2 | chr7 13032351 13032434 2 2 1 29 0 50 3 | chr7 13032566 13032641 2 2 1 35 0 50 4 | chr7 13032822 13033828 2 2 1 19 0 48 5 | chr7 13034043 13034634 2 2 1 13 0 49 6 | -------------------------------------------------------------------------------- /outrigger/tests/data/treutlein2014/unprocessed/sj_out_tab/SRR1033903_1.polyATrim.adapterTrim.rmRep.bamSJ.out.tab: -------------------------------------------------------------------------------- 1 | chr7 130164124 130167702 2 2 1 41 2 50 2 | chr7 130164216 130167702 2 2 1 0 2 11 3 | chr7 130167809 130169738 2 2 1 31 1 50 4 | chr7 130169877 130171611 2 2 1 36 0 49 5 | chr7 130171683 130172816 2 2 1 35 0 46 6 | chr7 130172940 130177674 2 2 1 33 0 49 7 | chr7 130177866 130180364 2 2 1 38 0 49 8 | chr7 130180476 130182640 2 2 1 22 0 47 9 | chr7 130182763 130185228 2 2 1 16 0 47 10 | chr7 130185381 130196171 0 0 1 14 0 43 11 | chr7 130196375 130199757 2 2 1 38 0 49 12 | chr7 130199906 130200982 2 2 1 32 0 48 13 | chr7 130201174 130218997 2 2 1 20 0 49 14 | chr7 130219122 130228622 2 2 1 18 0 39 15 | chr7 130228793 130261748 2 2 1 8 0 42 16 | chr7 130509259 130510810 2 2 1 27 0 48 17 | chr7 130510915 130513761 2 2 1 28 0 48 18 | chr7 130513825 130516104 2 2 1 37 0 50 19 | chr7 130516169 130519355 2 2 1 27 0 49 20 | chr7 130759641 130759914 1 1 1 3 0 25 21 | chr7 130760036 130764253 1 1 1 1 0 24 22 | -------------------------------------------------------------------------------- /outrigger/tests/data/treutlein2014/unprocessed/sj_out_tab/SRR1033904_1.polyATrim.adapterTrim.rmRep.bamSJ.out.tab: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/YeoLab/outrigger/9da86d2d8d137b309a53cae8851ba867cf757201/outrigger/tests/data/treutlein2014/unprocessed/sj_out_tab/SRR1033904_1.polyATrim.adapterTrim.rmRep.bamSJ.out.tab -------------------------------------------------------------------------------- /outrigger/tests/data/treutlein2014/unprocessed/sj_out_tab/SRR1033905_1.polyATrim.adapterTrim.rmRep.bamSJ.out.tab: -------------------------------------------------------------------------------- 1 | chr7 13029996 13030082 1 1 1 32 0 50 2 | chr7 13030207 13030288 1 1 1 29 0 50 3 | chr7 13030376 13030454 1 1 1 36 0 47 4 | chr7 13030593 13030688 1 1 1 53 0 50 5 | chr7 130509259 130510810 2 2 1 51 0 50 6 | chr7 130510915 130513761 2 2 1 44 0 48 7 | chr7 130513825 130516104 2 2 1 81 0 50 8 | chr7 130516169 130519876 2 2 1 58 0 50 9 | -------------------------------------------------------------------------------- /outrigger/tests/data/treutlein2014/unprocessed/sj_out_tab/SRR1033906_1.polyATrim.adapterTrim.rmRep.bamSJ.out.tab: -------------------------------------------------------------------------------- 1 | chr7 13032203 13032288 2 2 1 21 0 47 2 | chr7 13032351 13032434 2 2 1 13 0 45 3 | chr7 13032566 13032641 2 2 1 20 0 49 4 | chr7 13032822 13033828 2 2 1 16 0 49 5 | chr7 130751911 130753617 1 1 1 2 0 3 6 | chr7 130753662 130759164 1 1 1 5 0 44 7 | chr7 130759326 130759533 1 1 1 9 0 49 8 | chr7 130759641 130759914 1 1 1 9 0 50 9 | chr7 130760036 130764253 1 1 1 5 0 50 10 | -------------------------------------------------------------------------------- /outrigger/tests/data/treutlein2014/unprocessed/sj_out_tab/SRR1033907_1.polyATrim.adapterTrim.rmRep.bamSJ.out.tab: -------------------------------------------------------------------------------- 1 | chr7 13029125 13029206 1 1 1 1 2 4 2 | chr7 13030207 13030288 1 1 1 33 0 5 3 | chr7 13030376 13030454 1 1 1 62 0 50 4 | chr7 13030593 13030688 1 1 1 71 0 50 5 | chr7 130646431 130663015 1 1 0 10 0 47 6 | chr7 130663142 130674601 1 1 1 8 0 47 7 | chr7 130716840 130728522 1 1 1 1 0 30 8 | chr7 130751334 130751833 1 1 1 1 0 36 9 | chr7 130753662 130759164 1 1 1 1 0 15 10 | -------------------------------------------------------------------------------- /outrigger/tests/data/treutlein2014/unprocessed/sj_out_tab/SRR1033908_1.polyATrim.adapterTrim.rmRep.bamSJ.out.tab: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/YeoLab/outrigger/9da86d2d8d137b309a53cae8851ba867cf757201/outrigger/tests/data/treutlein2014/unprocessed/sj_out_tab/SRR1033908_1.polyATrim.adapterTrim.rmRep.bamSJ.out.tab -------------------------------------------------------------------------------- /outrigger/tests/data/treutlein2014/unprocessed/sj_out_tab/SRR1033909_1.polyATrim.adapterTrim.rmRep.bamSJ.out.tab: -------------------------------------------------------------------------------- 1 | chr7 13029996 13030082 1 1 1 7 0 42 2 | chr7 13030207 13030288 1 1 1 12 0 50 3 | chr7 13030376 13030454 1 1 1 8 0 48 4 | chr7 13030593 13030688 1 1 1 5 0 49 5 | chr7 13032203 13032288 2 2 1 1 0 13 6 | chr7 13034043 13034634 2 2 1 3 0 47 7 | chr7 130539966 130542679 2 2 1 1 0 16 8 | chr7 130759326 130759533 1 1 1 2 0 31 9 | chr7 130759641 130759914 1 1 1 2 0 34 10 | -------------------------------------------------------------------------------- /outrigger/tests/data/treutlein2014/unprocessed/sj_out_tab/SRR1033910_1.polyATrim.adapterTrim.rmRep.bamSJ.out.tab: -------------------------------------------------------------------------------- 1 | chr7 13032203 13032288 2 2 1 151 0 50 2 | chr7 13032351 13032434 2 2 1 191 0 50 3 | chr7 13032566 13032641 2 2 1 201 0 50 4 | chr7 13032822 13033828 2 2 1 111 0 50 5 | chr7 13034043 13034634 2 2 1 82 0 49 6 | chr7 130742302 130751189 1 1 0 14 0 47 7 | chr7 130751334 130751833 1 1 1 13 0 50 8 | chr7 130751911 130753617 1 1 1 15 0 44 9 | chr7 130753662 130759164 1 1 1 12 0 44 10 | chr7 130759326 130759533 1 1 1 9 0 47 11 | chr7 130759641 130759914 1 1 1 18 0 45 12 | chr7 130760036 130764253 1 1 1 19 0 49 13 | -------------------------------------------------------------------------------- /outrigger/tests/data/treutlein2014/unprocessed/sj_out_tab/SRR1033911_1.polyATrim.adapterTrim.rmRep.bamSJ.out.tab: -------------------------------------------------------------------------------- 1 | chr7 13028287 13031314 1 1 0 4 0 47 2 | chr7 13032203 13032288 2 2 1 48 0 50 3 | chr7 13032351 13032434 2 2 1 43 0 50 4 | chr7 13032566 13032641 2 2 1 42 0 49 5 | chr7 13032822 13033828 2 2 1 37 0 50 6 | chr7 13034043 13034634 2 2 1 29 0 49 7 | chr7 13035755 13035841 2 2 1 43 0 48 8 | chr7 13035906 13036211 2 2 1 44 0 48 9 | chr7 13036316 13036433 2 2 1 27 0 39 10 | chr7 13036473 13036565 2 2 1 29 0 40 11 | chr7 13036661 13037620 2 2 1 28 0 47 12 | chr7 130164124 130167702 2 2 1 27 2 46 13 | chr7 130164216 130167702 2 2 1 0 2 10 14 | chr7 130532693 130533576 2 2 1 75 0 50 15 | chr7 130533667 130533769 2 2 1 49 0 50 16 | chr7 130533862 130535523 2 2 1 62 0 50 17 | chr7 130535573 130536982 2 2 1 65 0 49 18 | chr7 130537078 130538161 2 2 1 43 0 50 19 | chr7 130538253 130539010 2 2 1 42 0 50 20 | chr7 130539111 130539813 2 2 1 59 0 49 21 | chr7 130539966 130542679 2 2 1 39 0 46 22 | chr7 130592766 130595818 2 2 0 1 0 27 23 | chr7 130739874 130740839 1 1 1 2 0 48 24 | chr7 130740956 130742129 1 1 1 1 0 25 25 | chr7 130759326 130759533 1 1 1 6 0 49 26 | chr7 130759641 130759914 1 1 1 4 0 43 27 | chr7 130760036 130764253 1 1 1 2 0 40 28 | -------------------------------------------------------------------------------- /outrigger/tests/data/treutlein2014/unprocessed/sj_out_tab/SRR1033912_1.polyATrim.adapterTrim.rmRep.bamSJ.out.tab: -------------------------------------------------------------------------------- 1 | chr7 13032203 13032288 2 2 1 59 0 50 2 | chr7 13032351 13032434 2 2 1 78 0 50 3 | chr7 13032566 13032641 2 2 1 74 0 46 4 | chr7 13032822 13033828 2 2 1 41 0 47 5 | chr7 13034043 13034634 2 2 1 28 0 50 6 | -------------------------------------------------------------------------------- /outrigger/tests/data/treutlein2014/unprocessed/sj_out_tab/SRR1033913_1.polyATrim.adapterTrim.rmRep.bamSJ.out.tab: -------------------------------------------------------------------------------- 1 | chr7 13032203 13032288 2 2 1 1 0 46 2 | chr7 13032566 13032641 2 2 1 2 0 44 3 | chr7 13032822 13033828 2 2 1 2 0 50 4 | chr7 13034043 13034634 2 2 1 1 0 21 5 | chr7 130457553 130457759 1 1 0 1 0 50 6 | chr7 130684827 130685364 1 1 0 0 12 40 7 | chr7 130684891 130684985 1 1 0 0 7 39 8 | chr7 130684891 130685208 1 1 0 0 9 35 9 | chr7 130684891 130685395 1 1 0 0 8 35 10 | chr7 130684970 130685034 1 1 0 1 0 49 11 | chr7 130685018 130685049 1 1 0 0 6 40 12 | chr7 130685050 130685208 1 1 0 0 5 35 13 | chr7 130685050 130685395 1 1 0 0 5 35 14 | chr7 130685114 130685208 1 1 0 0 5 35 15 | chr7 130685114 130685395 1 1 0 0 5 35 16 | chr7 130685209 130685458 1 1 0 0 3 23 17 | chr7 130685272 130685302 1 1 0 0 36 49 18 | chr7 130685272 130685395 1 1 0 0 52 49 19 | chr7 130685272 130685615 1 1 0 0 19 49 20 | chr7 130685365 130685426 1 1 0 0 1 34 21 | chr7 130685365 130685489 1 1 0 0 1 34 22 | chr7 130685365 130685552 1 1 0 0 1 34 23 | chr7 130685396 130685521 1 1 0 0 6 23 24 | chr7 130685585 130685615 1 1 0 0 49 49 25 | chr7 130760036 130764253 1 1 1 1 0 6 26 | -------------------------------------------------------------------------------- /outrigger/tests/data/treutlein2014/unprocessed/sj_out_tab/SRR1033914_1.polyATrim.adapterTrim.rmRep.bamSJ.out.tab: -------------------------------------------------------------------------------- 1 | chr7 13000083 13015969 1 1 0 1 0 25 2 | chr7 13032203 13032288 2 2 1 2 0 33 3 | chr7 13032351 13032434 2 2 1 1 0 6 4 | chr7 13032566 13032641 2 2 1 3 0 45 5 | chr7 13032822 13033828 2 2 1 5 0 50 6 | chr7 13034043 13034501 2 2 0 22 0 49 7 | chr7 13034043 13034634 2 2 1 2 0 45 8 | chr7 130164124 130167702 2 2 1 0 7 10 9 | chr7 130164216 130167702 2 2 1 84 7 50 10 | chr7 130167809 130169738 2 2 1 42 2 39 11 | chr7 130699646 130699820 2 2 0 1 0 21 12 | chr7 130877895 130882329 1 1 1 63 0 50 13 | chr7 130882387 130885402 1 1 1 61 0 46 14 | chr7 130885449 130892180 1 1 1 62 0 48 15 | chr7 130892279 130897324 1 1 1 62 0 49 16 | chr7 130897451 130900516 1 1 1 49 0 50 17 | chr7 130900661 130902176 1 1 1 54 0 48 18 | chr7 130902246 130904869 1 1 1 66 0 49 19 | chr7 130904935 130905390 1 1 1 60 0 50 20 | chr7 130905455 130908335 1 1 1 61 0 50 21 | chr7 130908426 130909587 1 1 1 56 0 42 22 | chr7 130909629 130910831 1 1 1 56 0 41 23 | -------------------------------------------------------------------------------- /outrigger/tests/data/treutlein2014/unprocessed/sj_out_tab/SRR1033915_1.polyATrim.adapterTrim.rmRep.bamSJ.out.tab: -------------------------------------------------------------------------------- 1 | chr7 130164124 130167702 2 2 1 143 12 50 2 | chr7 130164216 130167702 2 2 1 0 12 11 3 | chr7 130167809 130169738 2 2 1 141 3 50 4 | chr7 130169877 130171611 2 2 1 115 1 49 5 | chr7 130171683 130172816 2 2 1 115 0 46 6 | chr7 130172940 130177674 2 2 1 44 0 30 7 | chr7 130177866 130180364 2 2 1 1 0 14 8 | chr7 130180476 130182640 2 2 1 1 0 14 9 | -------------------------------------------------------------------------------- /outrigger/tests/data/treutlein2014/unprocessed/sj_out_tab/SRR1033916_1.polyATrim.adapterTrim.rmRep.bamSJ.out.tab: -------------------------------------------------------------------------------- 1 | chr7 130759326 130759533 1 1 1 2 0 46 2 | chr7 130759641 130759914 1 1 1 3 0 42 3 | chr7 130760036 130764253 1 1 1 4 0 37 4 | -------------------------------------------------------------------------------- /outrigger/tests/data/treutlein2014/unprocessed/sj_out_tab/SRR1033917_1.polyATrim.adapterTrim.rmRep.bamSJ.out.tab: -------------------------------------------------------------------------------- 1 | chr7 13029996 13030082 1 1 1 14 0 4 2 | chr7 13030207 13030288 1 1 1 46 0 50 3 | chr7 13030376 13030454 1 1 1 48 0 50 4 | chr7 13030593 13030688 1 1 1 42 0 49 5 | -------------------------------------------------------------------------------- /outrigger/tests/data/treutlein2014/unprocessed/sj_out_tab/SRR1033918_1.polyATrim.adapterTrim.rmRep.bamSJ.out.tab: -------------------------------------------------------------------------------- 1 | chr7 13028555 13028663 1 1 1 1 0 7 2 | chr7 13028779 13028880 1 1 1 3 0 47 3 | chr7 13028988 13029087 1 1 1 2 0 20 4 | chr7 13029125 13029206 1 1 1 2 0 37 5 | chr7 13029253 13029342 1 1 1 1 0 5 6 | chr7 13029996 13030082 1 1 1 5 0 47 7 | chr7 13030207 13030288 1 1 1 4 0 46 8 | chr7 13030376 13030454 1 1 1 8 0 40 9 | chr7 13030593 13030688 1 1 1 4 0 36 10 | chr7 13032203 13032288 2 2 1 2 0 38 11 | chr7 13032351 13032434 2 2 1 3 0 38 12 | chr7 13032566 13032641 2 2 1 11 0 49 13 | chr7 13032822 13033828 2 2 1 10 0 47 14 | chr7 13034043 13034634 2 2 1 24 0 49 15 | chr7 130172940 130177674 2 2 1 1 0 43 16 | chr7 130177866 130180364 2 2 1 1 0 23 17 | chr7 130509259 130510810 2 2 1 85 0 50 18 | chr7 130510915 130513761 2 2 1 95 0 48 19 | chr7 130513825 130516104 2 2 1 126 0 50 20 | chr7 130516169 130519355 2 2 1 95 0 50 21 | -------------------------------------------------------------------------------- /outrigger/tests/data/treutlein2014/unprocessed/sj_out_tab/SRR1033919_1.polyATrim.adapterTrim.rmRep.bamSJ.out.tab: -------------------------------------------------------------------------------- 1 | chr7 13032203 13032288 2 2 1 7 0 37 2 | chr7 13032351 13032434 2 2 1 13 0 50 3 | chr7 13032566 13032641 2 2 1 10 0 50 4 | chr7 13032566 13032791 2 2 0 1 0 24 5 | chr7 13032822 13033828 2 2 1 3 0 32 6 | chr7 13034043 13034634 2 2 1 15 0 49 7 | -------------------------------------------------------------------------------- /outrigger/tests/data/treutlein2014/unprocessed/sj_out_tab/SRR1033920_1.polyATrim.adapterTrim.rmRep.bamSJ.out.tab: -------------------------------------------------------------------------------- 1 | chr7 13027753 13027832 1 1 1 1 0 44 2 | chr7 13027950 13028020 1 1 1 1 0 18 3 | chr7 13028136 13028407 1 1 1 1 0 34 4 | chr7 13029253 13029342 1 1 1 8 0 34 5 | chr7 13029596 13029675 1 1 1 13 0 48 6 | chr7 13029996 13030082 1 1 1 18 0 47 7 | chr7 13030207 13030288 1 1 1 14 0 50 8 | chr7 13030376 13030454 1 1 1 16 0 48 9 | chr7 13030593 13030688 1 1 1 5 0 48 10 | chr7 13032203 13032288 2 2 1 1 0 34 11 | chr7 13032351 13032434 2 2 1 2 0 38 12 | chr7 13032566 13032641 2 2 1 1 0 12 13 | chr7 130646431 130674601 1 1 0 9 0 49 14 | chr7 130674740 130716702 1 1 1 4 0 42 15 | chr7 130716840 130728522 1 1 1 3 0 46 16 | chr7 130729829 130733505 1 1 0 16 0 49 17 | chr7 130733567 130734948 1 1 1 27 0 49 18 | chr7 130759641 130759914 1 1 1 45 0 47 19 | chr7 130760036 130764253 1 1 1 54 0 49 20 | -------------------------------------------------------------------------------- /outrigger/tests/data/treutlein2014/unprocessed/sj_out_tab/SRR1033921_1.polyATrim.adapterTrim.rmRep.bamSJ.out.tab: -------------------------------------------------------------------------------- 1 | chr7 13032203 13032288 2 2 1 80 0 50 2 | chr7 13032351 13032434 2 2 1 99 0 50 3 | chr7 13032566 13032641 2 2 1 43 0 49 4 | chr7 13032822 13033828 2 2 1 34 0 46 5 | chr7 13034043 13034634 2 2 1 22 0 50 6 | chr7 130164124 130167702 2 2 1 114 11 50 7 | chr7 130164216 130167702 2 2 1 0 11 11 8 | chr7 130167809 130169738 2 2 1 132 2 50 9 | chr7 130169877 130171611 2 2 1 92 0 50 10 | chr7 130171683 130172816 2 2 1 90 0 50 11 | chr7 130172940 130177674 2 2 1 42 0 50 12 | chr7 130177866 130180364 2 2 1 15 0 49 13 | chr7 130180476 130182640 2 2 1 11 0 48 14 | chr7 130182763 130185228 2 2 1 16 0 46 15 | chr7 130185381 130196171 0 0 1 17 0 48 16 | chr7 130196375 130200982 2 2 1 10 0 49 17 | chr7 130509259 130510810 2 2 1 20 0 49 18 | chr7 130510915 130513761 2 2 1 22 0 49 19 | chr7 130513825 130516104 2 2 1 23 0 50 20 | chr7 130516169 130519355 2 2 1 13 0 50 21 | -------------------------------------------------------------------------------- /outrigger/tests/data/treutlein2014/unprocessed/sj_out_tab/SRR1033922_1.polyATrim.adapterTrim.rmRep.bamSJ.out.tab: -------------------------------------------------------------------------------- 1 | chr7 13025417 13025643 1 1 1 44 0 49 2 | chr7 13025777 13027616 1 1 1 70 0 48 3 | chr7 13027753 13027832 1 1 1 33 0 50 4 | chr7 13027950 13028020 1 1 1 46 0 50 5 | chr7 13028136 13028407 1 1 1 43 0 50 6 | chr7 13028555 13028663 1 1 1 47 0 50 7 | chr7 13028779 13028880 1 1 1 41 0 50 8 | chr7 13028988 13029087 1 1 1 57 0 37 9 | chr7 13029125 13029206 1 1 1 52 0 38 10 | chr7 13029596 13029675 1 1 1 42 0 50 11 | chr7 13029996 13030082 1 1 1 49 0 50 12 | chr7 13030207 13030288 1 1 1 56 0 50 13 | chr7 13030376 13030454 1 1 1 60 0 50 14 | chr7 13030593 13030688 1 1 1 39 0 49 15 | -------------------------------------------------------------------------------- /outrigger/tests/data/treutlein2014/unprocessed/sj_out_tab/SRR1033923_1.polyATrim.adapterTrim.rmRep.bamSJ.out.tab: -------------------------------------------------------------------------------- 1 | chr7 13032203 13032288 2 2 1 86 0 50 2 | chr7 13032351 13032434 2 2 1 82 0 50 3 | chr7 130866001 130877733 1 1 1 59 0 49 4 | chr7 130877895 130882329 1 1 1 106 0 50 5 | chr7 130882387 130885402 1 1 1 103 0 46 6 | chr7 130885449 130892180 1 1 1 103 0 48 7 | chr7 130892246 130897324 1 1 0 63 0 49 8 | -------------------------------------------------------------------------------- /outrigger/tests/data/treutlein2014/unprocessed/sj_out_tab/SRR1033924_1.polyATrim.adapterTrim.rmRep.bamSJ.out.tab: -------------------------------------------------------------------------------- 1 | chr7 13029253 13029342 1 1 1 1 0 11 2 | chr7 13029596 13029675 1 1 1 2 0 42 3 | chr7 13029996 13030082 1 1 1 8 0 35 4 | chr7 13030207 13030288 1 1 1 7 0 40 5 | chr7 13030376 13030454 1 1 1 64 0 50 6 | chr7 13030593 13030688 1 1 1 87 0 49 7 | chr7 13032203 13032288 2 2 1 134 0 50 8 | chr7 13032351 13032434 2 2 1 147 0 50 9 | chr7 13032566 13032641 2 2 1 161 0 50 10 | chr7 13032822 13033828 2 2 1 103 0 50 11 | chr7 13034043 13034501 2 2 0 25 0 49 12 | chr7 13034043 13034634 2 2 1 51 0 49 13 | chr7 13035755 13035841 2 2 1 77 0 50 14 | chr7 13035906 13036211 2 2 1 86 0 49 15 | chr7 13036316 13036433 2 2 1 58 0 39 16 | chr7 13036473 13036565 2 2 1 60 0 40 17 | chr7 13036661 13037362 2 2 0 27 0 46 18 | chr7 13036661 13037620 2 2 1 17 0 49 19 | chr7 130509259 130510810 2 2 1 66 0 50 20 | chr7 130510915 130513761 2 2 1 48 0 50 21 | chr7 130513825 130516104 2 2 1 73 0 50 22 | chr7 130516169 130519355 2 2 1 56 0 50 23 | -------------------------------------------------------------------------------- /outrigger/tests/data/treutlein2014/unprocessed/sj_out_tab/SRR1033925_1.polyATrim.adapterTrim.rmRep.bamSJ.out.tab: -------------------------------------------------------------------------------- 1 | chr7 13030593 13030688 1 1 1 53 0 48 2 | chr7 13032203 13032288 2 2 1 68 0 50 3 | chr7 13032351 13032434 2 2 1 80 0 50 4 | chr7 13032566 13032641 2 2 1 6 0 45 5 | chr7 13032822 13033828 2 2 1 1 0 32 6 | chr7 130171683 130172816 2 2 1 2 0 29 7 | chr7 130177866 130180364 2 2 1 2 0 45 8 | chr7 130180476 130182640 2 2 1 3 0 35 9 | chr7 130182763 130185228 2 2 1 2 0 36 10 | chr7 130504823 130507481 2 2 1 58 0 48 11 | chr7 130507700 130509006 2 2 1 38 0 48 12 | chr7 130644589 130645467 2 2 0 18 0 48 13 | chr7 130645622 130645842 2 2 0 13 0 48 14 | -------------------------------------------------------------------------------- /outrigger/tests/data/treutlein2014/unprocessed/sj_out_tab/SRR1033926_1.polyATrim.adapterTrim.rmRep.bamSJ.out.tab: -------------------------------------------------------------------------------- 1 | chr7 13032203 13032288 2 2 1 64 0 50 2 | chr7 13032351 13032434 2 2 1 70 0 50 3 | chr7 13032566 13032641 2 2 1 84 0 50 4 | chr7 13032822 13033828 2 2 1 55 0 50 5 | chr7 13034043 13034634 2 2 1 40 0 49 6 | chr7 130164124 130167702 2 2 1 85 9 50 7 | chr7 130164216 130167702 2 2 1 0 9 11 8 | chr7 130167809 130169738 2 2 1 99 2 50 9 | chr7 130169877 130171611 2 2 1 84 1 47 10 | chr7 130171683 130172816 2 2 1 77 0 50 11 | chr7 130172940 130177674 2 2 1 62 0 50 12 | chr7 130177866 130180364 2 2 1 89 0 49 13 | chr7 130180476 130182640 2 2 1 62 0 50 14 | chr7 130182763 130185228 2 2 1 66 0 49 15 | chr7 130185381 130196177 2 2 1 64 0 49 16 | chr7 130196375 130199757 2 2 1 99 0 49 17 | chr7 130682011 130686814 2 4 0 56 2 50 18 | chr7 130687203 130703384 0 0 0 2 1 45 19 | -------------------------------------------------------------------------------- /outrigger/tests/data/treutlein2014/unprocessed/sj_out_tab/SRR1033927_1.polyATrim.adapterTrim.rmRep.bamSJ.out.tab: -------------------------------------------------------------------------------- 1 | chr7 13032203 13032288 2 2 1 191 0 50 2 | chr7 13032351 13032434 2 2 1 211 0 50 3 | chr7 13032566 13032641 2 2 1 207 0 50 4 | chr7 13032566 13033828 2 2 0 1 0 31 5 | chr7 13032822 13033828 2 2 1 146 0 50 6 | chr7 13034043 13034634 2 2 1 98 0 50 7 | chr7 130774719 130812993 1 1 0 1 0 19 8 | -------------------------------------------------------------------------------- /outrigger/tests/data/treutlein2014/unprocessed/sj_out_tab/SRR1033928_1.polyATrim.adapterTrim.rmRep.bamSJ.out.tab: -------------------------------------------------------------------------------- 1 | chr7 13006381 13007023 2 2 1 1 0 32 2 | chr7 13032203 13032288 2 2 1 33 0 50 3 | chr7 13032351 13032434 2 2 1 37 0 50 4 | chr7 13032566 13032641 2 2 1 37 0 46 5 | chr7 13032822 13033828 2 2 1 21 0 46 6 | chr7 13034043 13034501 2 2 0 13 0 45 7 | chr7 13034043 13034634 2 2 1 23 0 50 8 | -------------------------------------------------------------------------------- /outrigger/tests/data/treutlein2014/unprocessed/sj_out_tab/SRR1033929_1.polyATrim.adapterTrim.rmRep.bamSJ.out.tab: -------------------------------------------------------------------------------- 1 | chr7 130509259 130510810 2 2 1 20 0 50 2 | chr7 130510915 130513761 2 2 1 25 0 48 3 | chr7 130513825 130516104 2 2 1 24 0 50 4 | chr7 130516169 130519355 2 2 1 23 0 50 5 | chr7 130575140 130577437 1 1 0 14 0 49 6 | chr7 130577517 130601836 1 1 1 26 0 48 7 | chr7 130601938 130663015 1 1 1 29 0 48 8 | chr7 130663142 130674601 1 1 1 19 0 47 9 | chr7 130674740 130716702 1 1 1 7 0 47 10 | -------------------------------------------------------------------------------- /outrigger/tests/data/treutlein2014/unprocessed/sj_out_tab/SRR1033931_1.polyATrim.adapterTrim.rmRep.bamSJ.out.tab: -------------------------------------------------------------------------------- 1 | chr7 13034043 13034634 2 2 1 1 0 45 2 | -------------------------------------------------------------------------------- /outrigger/tests/data/treutlein2014/unprocessed/sj_out_tab/SRR1033932_1.polyATrim.adapterTrim.rmRep.bamSJ.out.tab: -------------------------------------------------------------------------------- 1 | chr7 13029596 13029675 1 1 1 4 0 47 2 | chr7 13029996 13030082 1 1 1 10 0 40 3 | chr7 13030207 13030288 1 1 1 7 0 37 4 | chr7 13030376 13030454 1 1 1 6 0 45 5 | chr7 13030593 13030688 1 1 1 6 0 41 6 | chr7 13032203 13032288 2 2 1 98 0 50 7 | chr7 13032351 13032434 2 2 1 109 0 48 8 | chr7 13032566 13032641 2 2 1 123 0 47 9 | -------------------------------------------------------------------------------- /outrigger/tests/data/treutlein2014/unprocessed/sj_out_tab/SRR1033933_1.polyATrim.adapterTrim.rmRep.bamSJ.out.tab: -------------------------------------------------------------------------------- 1 | chr7 13006381 13007023 2 2 1 35 0 41 2 | chr7 13032203 13032288 2 2 1 56 0 50 3 | chr7 13032351 13032434 2 2 1 79 0 50 4 | chr7 13032566 13032641 2 2 1 73 0 50 5 | chr7 13032822 13033828 2 2 1 50 0 50 6 | chr7 13034043 13034634 2 2 1 45 0 50 7 | chr7 130164124 130167702 2 2 1 0 2 9 8 | chr7 130164216 130167702 2 2 1 34 2 48 9 | chr7 130167809 130169738 2 2 1 13 2 39 10 | chr7 130533667 130533769 2 2 1 2 0 31 11 | chr7 130575140 130577437 1 1 0 3 0 19 12 | chr7 130577517 130601836 1 1 1 3 0 41 13 | chr7 130601938 130621720 1 1 1 2 0 19 14 | -------------------------------------------------------------------------------- /outrigger/tests/data/treutlein2014/unprocessed/sj_out_tab/SRR1033934_1.polyATrim.adapterTrim.rmRep.bamSJ.out.tab: -------------------------------------------------------------------------------- 1 | chr7 13032203 13032288 2 2 1 128 0 50 2 | chr7 13032351 13032434 2 2 1 146 0 50 3 | chr7 13032566 13032641 2 2 1 157 0 50 4 | chr7 13032822 13033828 2 2 1 116 0 50 5 | chr7 13034043 13034634 2 2 1 80 0 50 6 | chr7 130509259 130510810 2 2 1 127 0 50 7 | chr7 130510915 130513761 2 2 1 121 0 50 8 | chr7 130513825 130516104 2 2 1 162 0 50 9 | chr7 130516169 130519355 2 2 1 105 0 50 10 | chr7 130516169 130519876 2 2 1 22 0 50 11 | -------------------------------------------------------------------------------- /outrigger/tests/data/treutlein2014/unprocessed/sj_out_tab/SRR1033939_1.polyATrim.adapterTrim.rmRep.bamSJ.out.tab: -------------------------------------------------------------------------------- 1 | chr7 13029253 13029342 1 1 1 13 0 29 2 | chr7 13029596 13029675 1 1 1 31 0 49 3 | chr7 13029996 13030082 1 1 1 48 0 50 4 | chr7 13030207 13030288 1 1 1 42 0 50 5 | chr7 13030376 13030454 1 1 1 34 0 50 6 | chr7 13030593 13030688 1 1 1 29 0 50 7 | chr7 13034043 13034634 2 2 1 1 0 50 8 | chr7 130164124 130167702 2 2 1 1 0 41 9 | chr7 130164216 130167702 2 2 1 12 0 50 10 | chr7 130167809 130169738 2 2 1 5 0 37 11 | chr7 130196375 130200982 2 2 1 4 0 39 12 | chr7 130201174 130218997 2 2 1 6 0 35 13 | chr7 130219122 130228622 2 2 1 2 0 42 14 | chr7 130228793 130241199 2 2 1 6 0 47 15 | chr7 130241278 130261748 2 2 1 7 0 34 16 | chr7 130394737 130418447 2 2 1 23 0 49 17 | chr7 130418569 130464130 2 2 1 23 0 50 18 | chr7 130464231 130467255 2 2 1 22 0 47 19 | chr7 130467438 130481682 2 2 1 11 0 33 20 | chr7 130481716 130504693 2 2 1 14 0 33 21 | chr7 130504823 130507481 2 2 1 9 0 44 22 | chr7 130507700 130509006 2 2 1 10 0 40 23 | chr7 130509259 130510810 2 2 1 7 0 29 24 | chr7 130510915 130513761 2 2 1 9 0 25 25 | chr7 130513825 130516104 2 2 1 12 0 50 26 | chr7 130516169 130519355 2 2 1 9 0 50 27 | chr7 130753662 130759164 1 1 1 2 0 30 28 | chr7 130759326 130759533 1 1 1 2 0 42 29 | chr7 130759641 130759914 1 1 1 1 0 43 30 | chr7 130760036 130764253 1 1 1 1 0 49 31 | chr7 130874941 130877006 1 1 0 1 0 32 32 | -------------------------------------------------------------------------------- /outrigger/tests/data/treutlein2014/unprocessed/sj_out_tab/SRR1033941_1.polyATrim.adapterTrim.rmRep.bamSJ.out.tab: -------------------------------------------------------------------------------- 1 | chr7 13025417 13025643 1 1 1 50 0 50 2 | chr7 13025777 13027616 1 1 1 75 0 48 3 | chr7 13027753 13027832 1 1 1 49 0 49 4 | chr7 13027950 13028020 1 1 1 37 0 50 5 | chr7 13028136 13028407 1 1 1 32 0 50 6 | chr7 13028555 13028663 1 1 1 39 0 50 7 | chr7 13028779 13028880 1 1 1 51 0 48 8 | chr7 13028988 13029087 1 1 1 50 0 37 9 | chr7 13029125 13029206 1 1 1 38 0 37 10 | chr7 13029253 13029342 1 1 1 39 0 46 11 | chr7 13029596 13029675 1 1 1 40 0 47 12 | chr7 13029996 13030082 1 1 1 63 0 50 13 | chr7 13030207 13030288 1 1 1 55 0 50 14 | chr7 13030376 13030454 1 1 1 48 0 49 15 | chr7 13030593 13030688 1 1 1 50 0 50 16 | chr7 130164124 130167702 2 2 1 1 0 15 17 | chr7 130164216 130167702 2 2 1 1 0 47 18 | chr7 130185381 130196177 2 2 1 24 1 48 19 | chr7 130509259 130510810 2 2 1 34 0 50 20 | chr7 130510915 130513761 2 2 1 35 0 43 21 | chr7 130513825 130516104 2 2 1 71 0 50 22 | chr7 130516169 130519355 2 2 1 39 0 50 23 | chr7 130516169 130519876 2 2 1 1 0 49 24 | chr7 130532693 130533576 2 2 1 8 0 47 25 | chr7 130533667 130533769 2 2 1 9 0 46 26 | chr7 130533862 130535523 2 2 1 7 0 46 27 | chr7 130535573 130536982 2 2 1 6 0 47 28 | chr7 130537078 130538161 2 2 1 9 0 50 29 | chr7 130538253 130539010 2 2 1 7 0 47 30 | chr7 130539111 130539813 2 2 1 5 0 40 31 | chr7 130539966 130542679 2 2 1 6 0 42 32 | chr7 130542811 130545894 2 2 1 6 0 47 33 | chr7 130545973 130546991 2 2 1 5 0 41 34 | -------------------------------------------------------------------------------- /outrigger/tests/data/treutlein2014/unprocessed/sj_out_tab/SRR1033944_1.polyATrim.adapterTrim.rmRep.bamSJ.out.tab: -------------------------------------------------------------------------------- 1 | chr7 13030593 13030688 1 1 1 32 0 13 2 | chr7 13032203 13032288 2 2 1 59 0 50 3 | chr7 13032351 13032434 2 2 1 74 0 48 4 | chr7 13032566 13032641 2 2 1 98 0 46 5 | chr7 13032822 13033828 2 2 1 43 0 49 6 | chr7 13034043 13034634 2 2 1 30 0 49 7 | chr7 130172940 130177674 2 2 1 1 0 34 8 | chr7 130177866 130180364 2 2 1 2 0 44 9 | chr7 130182763 130185228 2 2 1 1 0 31 10 | chr7 130457478 130457561 1 1 0 0 1 33 11 | chr7 130457478 130457645 1 1 0 1 1 47 12 | chr7 130457478 130457693 1 1 0 1 0 38 13 | chr7 130457478 130457711 1 1 0 0 1 17 14 | chr7 130457517 130457666 1 3 0 0 1 45 15 | chr7 130457553 130457654 1 1 0 0 1 33 16 | chr7 130457553 130457882 1 1 0 0 1 33 17 | chr7 130457580 130457711 1 1 0 1 0 41 18 | chr7 130509259 130510810 2 2 1 1 0 19 19 | chr7 130510915 130513761 2 2 1 2 0 19 20 | chr7 130513825 130516104 2 2 1 3 0 44 21 | chr7 130516169 130519355 2 2 1 2 0 27 22 | chr7 130751334 130751833 1 1 1 1 0 6 23 | chr7 130751911 130753617 1 1 1 1 0 20 24 | chr7 130753662 130759164 1 1 1 1 0 37 25 | chr7 130759326 130759533 1 1 1 1 0 49 26 | chr7 130759641 130759914 1 1 1 1 0 14 27 | -------------------------------------------------------------------------------- /outrigger/tests/data/treutlein2014/unprocessed/sj_out_tab/SRR1033945_1.polyATrim.adapterTrim.rmRep.bamSJ.out.tab: -------------------------------------------------------------------------------- 1 | chr7 13030376 13030454 1 1 1 3 0 29 2 | chr7 13030593 13030688 1 1 1 77 0 50 3 | chr7 130164216 130167702 2 2 1 1 0 31 4 | chr7 130201174 130218997 2 2 1 1 0 12 5 | chr7 130219122 130228622 2 2 1 1 0 35 6 | chr7 130509259 130510810 2 2 1 1 0 19 7 | chr7 130510915 130513761 2 2 1 2 0 25 8 | chr7 130513825 130516104 2 2 1 3 0 49 9 | chr7 130516169 130519355 2 2 1 1 0 32 10 | chr7 130516169 130519876 2 2 1 1 0 28 11 | chr7 130751334 130751833 1 1 1 1 0 6 12 | chr7 130751911 130753617 1 1 1 1 0 10 13 | chr7 130753662 130759164 1 1 1 1 0 44 14 | chr7 130759326 130759533 1 1 1 2 0 49 15 | chr7 130759641 130759914 1 1 1 1 0 42 16 | chr7 130760036 130764253 1 1 1 1 0 23 17 | -------------------------------------------------------------------------------- /outrigger/tests/data/treutlein2014/unprocessed/sj_out_tab/SRR1033947_1.polyATrim.adapterTrim.rmRep.bamSJ.out.tab: -------------------------------------------------------------------------------- 1 | chr7 13032203 13032288 2 2 1 3 0 50 2 | chr7 13032351 13032434 2 2 1 1 0 4 3 | chr7 130509259 130510810 2 2 1 5 0 36 4 | chr7 130510915 130513761 2 2 1 3 0 48 5 | chr7 130513825 130516104 2 2 1 4 0 50 6 | chr7 130516169 130519355 2 2 1 3 0 32 7 | chr7 130760036 130764253 1 1 1 1 0 4 8 | -------------------------------------------------------------------------------- /outrigger/tests/data/treutlein2014/unprocessed/sj_out_tab/SRR1033952_1.polyATrim.adapterTrim.rmRep.bamSJ.out.tab: -------------------------------------------------------------------------------- 1 | chr7 13029996 13030082 1 1 1 16 0 50 2 | chr7 13030207 13030288 1 1 1 25 0 50 3 | chr7 13030376 13030454 1 1 1 29 0 47 4 | chr7 13030593 13030688 1 1 1 25 0 42 5 | chr7 13032203 13032288 2 2 1 69 0 50 6 | chr7 13032351 13032434 2 2 1 81 0 48 7 | chr7 13032566 13032641 2 2 1 72 0 50 8 | chr7 13032822 13033828 2 2 1 62 0 50 9 | chr7 13034043 13034501 2 2 0 8 0 50 10 | chr7 13034043 13034634 2 2 1 29 0 49 11 | chr7 130164124 130167702 2 2 1 0 1 8 12 | chr7 130164216 130167702 2 2 1 14 1 50 13 | chr7 130167809 130169738 2 2 1 3 0 22 14 | chr7 130169877 130171611 2 2 1 1 0 4 15 | chr7 130171683 130172816 2 2 1 2 0 46 16 | chr7 130177866 130180364 2 2 1 1 0 9 17 | chr7 130180476 130185228 2 2 0 1 0 15 18 | chr7 130196375 130199757 2 2 1 1 0 34 19 | chr7 130509259 130510810 2 2 1 4 0 29 20 | chr7 130510915 130513761 2 2 1 4 0 16 21 | chr7 130510915 130516104 2 2 0 1 0 29 22 | chr7 130513825 130516104 2 2 1 6 0 50 23 | chr7 130516169 130519355 2 2 1 3 0 36 24 | chr7 130516169 130519876 2 2 1 3 0 31 25 | chr7 130532693 130533576 2 2 1 27 0 50 26 | chr7 130533667 130533769 2 2 1 15 0 41 27 | chr7 130533862 130535523 2 2 1 27 0 50 28 | chr7 130535573 130536982 2 2 1 22 0 49 29 | chr7 130537078 130538161 2 2 1 20 0 50 30 | chr7 130538253 130539010 2 2 1 29 0 50 31 | chr7 130601938 130674601 1 1 0 2 0 44 32 | chr7 130674740 130716702 1 1 1 2 0 29 33 | chr7 130716840 130728522 1 1 1 2 0 49 34 | chr7 130735229 130739811 1 1 1 1 0 8 35 | chr7 130739874 130740839 1 1 1 2 0 36 36 | chr7 130740956 130742129 1 1 1 2 0 36 37 | chr7 130760036 130764253 1 1 1 1 0 16 38 | -------------------------------------------------------------------------------- /outrigger/tests/data/treutlein2014/unprocessed/sj_out_tab/SRR1033953_1.polyATrim.adapterTrim.rmRep.bamSJ.out.tab: -------------------------------------------------------------------------------- 1 | chr7 13028136 13028407 1 1 1 1 0 46 2 | chr7 13029253 13029342 1 1 1 1 0 26 3 | chr7 13029596 13029675 1 1 1 17 0 45 4 | chr7 13029996 13030082 1 1 1 36 0 47 5 | chr7 13030207 13030288 1 1 1 39 0 50 6 | chr7 13030376 13030454 1 1 1 75 0 50 7 | chr7 13030593 13030688 1 1 1 86 0 50 8 | chr7 13032203 13032288 2 2 1 47 0 50 9 | chr7 13032351 13032434 2 2 1 49 0 50 10 | chr7 13032566 13032641 2 2 1 10 0 42 11 | chr7 13032566 13032791 2 2 0 24 0 31 12 | chr7 13032822 13033828 2 2 1 37 0 40 13 | chr7 13034043 13034501 2 2 0 1 0 40 14 | chr7 13034043 13034634 2 2 1 18 0 46 15 | chr7 130164124 130167702 2 2 1 0 1 7 16 | chr7 130164216 130167702 2 2 1 12 1 50 17 | chr7 130167809 130169738 2 2 1 9 0 39 18 | chr7 130509259 130510810 2 2 1 46 0 42 19 | chr7 130510915 130513761 2 2 1 41 0 49 20 | chr7 130513825 130516104 2 2 1 56 0 50 21 | chr7 130516169 130519355 2 2 1 40 0 50 22 | chr7 130865984 130877733 1 1 1 2 0 43 23 | chr7 130877895 130882329 1 1 1 3 0 50 24 | chr7 130882387 130885402 1 1 1 3 0 38 25 | chr7 130885449 130892180 1 1 1 3 0 41 26 | chr7 130892279 130897324 1 1 1 2 0 36 27 | chr7 130897451 130900516 1 1 1 2 0 33 28 | chr7 130900661 130902176 1 1 1 2 0 47 29 | chr7 130902246 130904869 1 1 1 4 0 47 30 | chr7 130904935 130905390 1 1 1 2 0 39 31 | chr7 130905455 130908335 1 1 1 1 0 8 32 | chr7 130908426 130909587 1 1 1 2 0 37 33 | chr7 130909629 130910831 1 1 1 1 0 29 34 | -------------------------------------------------------------------------------- /outrigger/tests/data/treutlein2014/unprocessed/sj_out_tab/SRR1033954_1.polyATrim.adapterTrim.rmRep.bamSJ.out.tab: -------------------------------------------------------------------------------- 1 | chr7 13028779 13028880 1 1 1 1 0 17 2 | chr7 13028920 13028952 1 1 0 1 0 26 3 | chr7 13028988 13029087 1 1 1 1 0 35 4 | chr7 13029125 13029206 1 1 1 1 0 3 5 | chr7 13029253 13029342 1 1 1 1 0 18 6 | chr7 13029996 13030082 1 1 1 3 0 34 7 | chr7 13030207 13030288 1 1 1 5 0 45 8 | chr7 13030376 13030454 1 1 1 4 0 50 9 | chr7 13030593 13030688 1 1 1 3 0 45 10 | chr7 13032071 13032633 1 1 0 1 0 32 11 | chr7 13032203 13032288 2 2 1 80 0 50 12 | chr7 13032351 13032434 2 2 1 72 0 50 13 | chr7 13032566 13032641 2 2 1 120 0 49 14 | chr7 13032822 13033828 2 2 1 94 0 49 15 | chr7 13034043 13034634 2 2 1 76 0 49 16 | chr7 130164124 130167702 2 2 1 33 1 48 17 | chr7 130164216 130167702 2 2 1 0 1 6 18 | chr7 130167809 130169738 2 2 1 30 0 50 19 | chr7 130169877 130171611 2 2 1 32 1 49 20 | chr7 130171683 130172816 2 2 1 27 0 46 21 | chr7 130172940 130177674 2 2 1 18 0 49 22 | chr7 130177866 130180364 2 2 1 24 0 47 23 | chr7 130180476 130182640 2 2 1 12 0 49 24 | chr7 130182763 130185228 2 2 1 13 0 50 25 | chr7 130185381 130196177 2 2 1 13 0 48 26 | chr7 130185851 130186554 2 2 0 2 0 30 27 | chr7 130199657 130200219 2 4 0 12 0 45 28 | chr7 130503851 130507481 2 2 1 32 1 47 29 | chr7 130504823 130507481 2 2 1 0 1 5 30 | chr7 130507700 130509006 2 2 1 25 0 48 31 | chr7 130509259 130510810 2 2 1 62 0 50 32 | chr7 130510915 130513761 2 2 1 69 0 48 33 | chr7 130513825 130516104 2 2 1 61 0 50 34 | chr7 130533862 130535523 2 2 1 1 0 19 35 | chr7 130537078 130538161 2 2 1 1 0 9 36 | chr7 130759326 130759533 1 1 1 11 0 49 37 | chr7 130759641 130759914 1 1 1 13 0 47 38 | chr7 130760036 130764253 1 1 1 11 0 46 39 | -------------------------------------------------------------------------------- /outrigger/tests/data/treutlein2014/unprocessed/sj_out_tab/SRR1033955_1.polyATrim.adapterTrim.rmRep.bamSJ.out.tab: -------------------------------------------------------------------------------- 1 | chr7 13025777 13027616 1 1 1 2 0 23 2 | chr7 13027753 13027832 1 1 1 27 0 15 3 | chr7 13027950 13028020 1 1 1 36 0 49 4 | chr7 13028136 13028407 1 1 1 41 0 50 5 | chr7 13028555 13028663 1 1 1 69 0 49 6 | chr7 13028779 13028880 1 1 1 75 0 49 7 | chr7 13028988 13029087 1 1 1 120 1 45 8 | chr7 13029125 13029206 1 1 1 108 1 38 9 | chr7 13029253 13029342 1 1 1 88 0 47 10 | chr7 13029596 13029675 1 1 1 60 0 48 11 | chr7 13029996 13030082 1 1 1 84 0 50 12 | chr7 13030207 13030288 1 1 1 80 0 50 13 | chr7 13030376 13030454 1 1 1 92 0 50 14 | chr7 13030593 13030688 1 1 1 146 0 50 15 | chr7 130164124 130167702 2 2 1 22 1 50 16 | chr7 130164216 130167702 2 2 1 0 1 10 17 | chr7 130167809 130169738 2 2 1 13 0 39 18 | chr7 130509259 130510810 2 2 1 49 0 50 19 | chr7 130510915 130513761 2 2 1 52 0 49 20 | chr7 130513825 130516104 2 2 1 64 0 50 21 | chr7 130516169 130519355 2 2 1 46 0 50 22 | chr7 130759326 130759533 1 1 1 19 0 5 23 | chr7 130759641 130759914 1 1 1 37 0 50 24 | chr7 130760036 130764253 1 1 1 47 0 50 25 | -------------------------------------------------------------------------------- /outrigger/tests/data/treutlein2014/unprocessed/sj_out_tab/SRR1033956_1.polyATrim.adapterTrim.rmRep.bamSJ.out.tab: -------------------------------------------------------------------------------- 1 | chr7 13025062 13025303 1 1 1 2 0 41 2 | chr7 13025417 13025643 1 1 1 34 0 50 3 | chr7 13025777 13027616 1 1 1 45 0 50 4 | chr7 13027753 13027832 1 1 1 33 0 49 5 | chr7 13027950 13028020 1 1 1 31 0 46 6 | chr7 13028136 13028407 1 1 1 20 0 47 7 | chr7 13028555 13028663 1 1 1 26 0 48 8 | chr7 13028779 13028880 1 1 1 38 0 48 9 | chr7 13028988 13029087 1 1 1 53 0 37 10 | chr7 13029125 13029206 1 1 1 53 0 39 11 | chr7 13029253 13029342 1 1 1 57 0 43 12 | chr7 13029596 13029675 1 1 1 25 0 47 13 | chr7 13029996 13030082 1 1 1 70 0 46 14 | chr7 13030207 13030288 1 1 1 90 0 50 15 | chr7 13030376 13030454 1 1 1 94 0 48 16 | chr7 13030593 13030688 1 1 1 72 0 49 17 | chr7 13032203 13032288 2 2 1 25 0 49 18 | chr7 13032351 13032434 2 2 1 28 0 50 19 | chr7 13032566 13032641 2 2 1 32 0 47 20 | chr7 13032822 13033828 2 2 1 27 0 49 21 | chr7 13034043 13034634 2 2 1 21 0 49 22 | chr7 130164124 130167702 2 2 1 31 0 47 23 | chr7 130167809 130169738 2 2 1 27 0 39 24 | chr7 130169877 130171611 2 2 1 17 0 49 25 | chr7 130171683 130172816 2 2 1 12 0 47 26 | chr7 130172940 130177674 2 2 1 10 0 47 27 | chr7 130177866 130180364 2 2 1 4 0 49 28 | chr7 130180476 130182640 2 2 1 4 0 47 29 | chr7 130532693 130533576 2 2 1 2 0 17 30 | chr7 130897451 130900516 1 1 1 14 0 49 31 | chr7 130900661 130902176 1 1 1 14 0 48 32 | chr7 130902246 130904869 1 1 1 20 0 47 33 | chr7 130981772 130982236 1 1 1 1 0 8 34 | chr7 130982295 130983659 1 1 1 1 0 35 35 | -------------------------------------------------------------------------------- /outrigger/tests/data/treutlein2014/unprocessed/sj_out_tab/SRR1033957_1.polyATrim.adapterTrim.rmRep.bamSJ.out.tab: -------------------------------------------------------------------------------- 1 | chr7 13029996 13030082 1 1 1 43 0 46 2 | chr7 13030207 13030288 1 1 1 40 0 48 3 | chr7 13030376 13030454 1 1 1 42 0 48 4 | chr7 13030593 13030688 1 1 1 45 0 50 5 | chr7 13032203 13032288 2 2 1 28 0 50 6 | chr7 13032351 13032434 2 2 1 36 0 50 7 | chr7 13032566 13032641 2 2 1 41 0 49 8 | chr7 13032822 13033828 2 2 1 26 0 49 9 | chr7 13034043 13034634 2 2 1 8 0 26 10 | chr7 130164124 130167702 2 2 1 1 0 42 11 | chr7 130509259 130510810 2 2 1 28 0 42 12 | chr7 130510915 130513761 2 2 1 41 0 49 13 | chr7 130513825 130516104 2 2 1 67 0 50 14 | chr7 130516169 130519355 2 2 1 91 0 50 15 | chr7 130516169 130519876 2 2 1 8 0 50 16 | chr7 130532693 130533576 2 2 1 57 0 49 17 | chr7 130533667 130533769 2 2 1 54 0 49 18 | chr7 130533862 130535523 2 2 1 39 0 49 19 | chr7 130535573 130536982 2 2 1 36 0 49 20 | chr7 130537078 130538161 2 2 1 33 0 50 21 | chr7 130538253 130539010 2 2 1 38 0 45 22 | chr7 130539111 130539813 2 2 1 5 0 31 23 | -------------------------------------------------------------------------------- /outrigger/tests/data/treutlein2014/unprocessed/sj_out_tab/SRR1033958_1.polyATrim.adapterTrim.rmRep.bamSJ.out.tab: -------------------------------------------------------------------------------- 1 | chr7 13028779 13028880 1 1 1 34 0 49 2 | chr7 13028988 13029087 1 1 1 36 0 37 3 | chr7 13029125 13029206 1 1 1 46 0 38 4 | chr7 13029253 13029342 1 1 1 52 0 48 5 | chr7 13029596 13029675 1 1 1 23 0 47 6 | chr7 13029996 13030082 1 1 1 47 0 47 7 | chr7 13030207 13030288 1 1 1 45 0 50 8 | chr7 13030376 13030454 1 1 1 42 0 47 9 | chr7 13030593 13030688 1 1 1 27 0 49 10 | chr7 13032203 13032288 2 2 1 16 0 46 11 | chr7 13032351 13032434 2 2 1 31 0 48 12 | chr7 13032566 13032641 2 2 1 31 0 49 13 | chr7 13032822 13033828 2 2 1 15 0 46 14 | chr7 13034043 13034634 2 2 1 5 0 47 15 | chr7 130164124 130167702 2 2 1 5 0 46 16 | chr7 130167809 130169738 2 2 1 6 0 50 17 | chr7 130169877 130171611 2 2 1 4 0 50 18 | chr7 130171683 130172816 2 2 1 6 0 34 19 | chr7 130172940 130177674 2 2 1 8 0 49 20 | chr7 130177866 130180364 2 2 1 1 0 23 21 | chr7 130507700 130509006 2 2 1 1 0 15 22 | chr7 130509259 130510810 2 2 1 7 0 33 23 | chr7 130510915 130513761 2 2 1 3 0 32 24 | chr7 130513825 130516104 2 2 1 5 0 50 25 | chr7 130516169 130519355 2 2 1 4 0 50 26 | -------------------------------------------------------------------------------- /outrigger/tests/data/treutlein2014/unprocessed/sj_out_tab/SRR1033959_1.polyATrim.adapterTrim.rmRep.bamSJ.out.tab: -------------------------------------------------------------------------------- 1 | chr7 13029596 13029675 1 1 1 52 0 49 2 | chr7 13029996 13030082 1 1 1 92 0 49 3 | chr7 13030207 13030288 1 1 1 68 0 50 4 | chr7 13030376 13030454 1 1 1 81 0 50 5 | chr7 13030593 13030688 1 1 1 85 0 50 6 | chr7 13032203 13032288 2 2 1 65 0 42 7 | chr7 13032351 13032434 2 2 1 104 0 50 8 | chr7 13032566 13032641 2 2 1 90 0 46 9 | chr7 13032822 13033828 2 2 1 72 0 50 10 | chr7 13034043 13034634 2 2 1 51 0 50 11 | chr7 13035755 13035841 2 2 1 1 0 14 12 | chr7 130164124 130167702 2 2 1 127 6 50 13 | chr7 130164216 130167702 2 2 1 5 6 50 14 | chr7 130167809 130169738 2 2 1 120 2 50 15 | chr7 130169877 130171611 2 2 1 103 0 49 16 | chr7 130171683 130172816 2 2 1 95 0 50 17 | chr7 130172940 130177674 2 2 1 60 0 49 18 | chr7 130177866 130180364 2 2 1 52 0 48 19 | chr7 130180476 130182640 2 2 1 29 0 29 20 | chr7 130394737 130418447 2 2 1 7 0 47 21 | chr7 130509259 130510810 2 2 1 2 0 41 22 | chr7 130510915 130513761 2 2 1 2 0 17 23 | chr7 130513825 130516104 2 2 1 3 0 50 24 | chr7 130516169 130519355 2 2 1 3 0 50 25 | chr7 130877895 130882329 1 1 1 5 0 43 26 | chr7 130882387 130885402 1 1 1 5 0 46 27 | chr7 130885449 130892180 1 1 1 5 0 48 28 | chr7 130892279 130897324 1 1 1 15 0 47 29 | chr7 130897451 130900516 1 1 1 4 0 49 30 | chr7 130900661 130902176 1 1 1 17 0 49 31 | chr7 130902246 130904869 1 1 1 19 0 49 32 | chr7 130904935 130905390 1 1 1 11 0 45 33 | chr7 130905455 130908335 1 1 1 9 0 32 34 | chr7 130908426 130909587 1 1 1 5 0 38 35 | chr7 130909629 130910831 1 1 1 10 0 41 36 | -------------------------------------------------------------------------------- /outrigger/tests/data/treutlein2014/unprocessed/sj_out_tab/SRR1033960_1.polyATrim.adapterTrim.rmRep.bamSJ.out.tab: -------------------------------------------------------------------------------- 1 | chr7 13028988 13029087 1 1 1 1 0 37 2 | chr7 13029125 13029206 1 1 1 1 0 15 3 | chr7 13029253 13029342 1 1 1 1 0 42 4 | chr7 13030376 13030454 1 1 1 3 0 40 5 | chr7 13032203 13032288 2 2 1 52 0 50 6 | chr7 13032351 13032434 2 2 1 49 0 50 7 | chr7 13032566 13032641 2 2 1 6 0 44 8 | chr7 130163931 130167702 2 2 0 42 0 49 9 | chr7 130164124 130167702 2 2 1 1 1 45 10 | chr7 130164216 130167702 2 2 1 0 1 7 11 | chr7 130167809 130169738 2 2 1 33 0 48 12 | chr7 130169877 130171611 2 2 1 21 0 17 13 | chr7 130865984 130877733 1 1 1 24 0 43 14 | chr7 130877895 130882329 1 1 1 17 1 8 15 | chr7 130882387 130885402 1 1 1 34 3 46 16 | chr7 130885449 130892180 1 1 1 52 2 48 17 | chr7 130892279 130897324 1 1 1 54 1 49 18 | chr7 130897451 130900516 1 1 1 47 0 50 19 | chr7 130900661 130902176 1 1 1 26 0 49 20 | chr7 130902246 130904869 1 1 1 1 0 5 21 | -------------------------------------------------------------------------------- /outrigger/tests/data/treutlein2014/unprocessed/sj_out_tab/SRR1033962_1.polyATrim.adapterTrim.rmRep.bamSJ.out.tab: -------------------------------------------------------------------------------- 1 | chr7 13029996 13030082 1 1 1 29 0 42 2 | chr7 13030207 13030288 1 1 1 26 0 50 3 | chr7 13030376 13030454 1 1 1 41 0 50 4 | chr7 13030593 13030688 1 1 1 45 0 49 5 | chr7 13032203 13032288 2 2 1 11 0 49 6 | chr7 13032351 13032434 2 2 1 9 0 48 7 | chr7 13032566 13032641 2 2 1 5 0 43 8 | chr7 13032822 13033828 2 2 1 3 0 46 9 | chr7 13034043 13034501 2 2 0 1 0 45 10 | chr7 13034043 13034634 2 2 1 4 0 43 11 | chr7 130164124 130167702 2 2 1 17 2 49 12 | chr7 130164216 130167702 2 2 1 1 2 24 13 | chr7 130167809 130169738 2 2 1 18 0 39 14 | chr7 130507700 130509006 2 2 1 13 0 32 15 | chr7 130509259 130510810 2 2 1 60 0 50 16 | chr7 130510915 130513761 2 2 1 91 0 48 17 | chr7 130513825 130516104 2 2 1 93 0 50 18 | chr7 130516169 130519355 2 2 1 59 0 50 19 | chr7 130532693 130533576 2 2 1 11 0 47 20 | chr7 130533667 130533769 2 2 1 12 0 34 21 | chr7 130533862 130535523 2 2 1 2 0 14 22 | chr7 130535573 130536982 2 2 1 2 0 38 23 | chr7 130538253 130539010 2 2 1 2 0 45 24 | chr7 130885449 130892180 1 1 1 5 0 19 25 | chr7 130892279 130897324 1 1 1 9 0 49 26 | chr7 130983756 130984962 1 1 1 5 0 50 27 | -------------------------------------------------------------------------------- /outrigger/tests/data/treutlein2014/unprocessed/sj_out_tab/SRR1033963_1.polyATrim.adapterTrim.rmRep.bamSJ.out.tab: -------------------------------------------------------------------------------- 1 | chr7 13029253 13029342 1 1 1 1 0 27 2 | chr7 13029596 13029675 1 1 1 3 0 48 3 | chr7 13029996 13030082 1 1 1 2 0 34 4 | chr7 13030207 13030288 1 1 1 5 0 46 5 | chr7 13030376 13030454 1 1 1 32 0 49 6 | chr7 13030593 13030688 1 1 1 53 0 50 7 | chr7 13032203 13032288 2 2 1 4 0 38 8 | chr7 13032351 13032434 2 2 1 3 0 43 9 | chr7 13032566 13032641 2 2 1 4 0 40 10 | chr7 13032822 13033828 2 2 1 5 0 46 11 | chr7 130509259 130510810 2 2 1 1 0 27 12 | chr7 130513825 130516104 2 2 1 1 0 50 13 | chr7 130885449 130892180 1 1 1 1 0 14 14 | -------------------------------------------------------------------------------- /outrigger/tests/data/treutlein2014/unprocessed/sj_out_tab/SRR1033964_1.polyATrim.adapterTrim.rmRep.bamSJ.out.tab: -------------------------------------------------------------------------------- 1 | chr7 13029253 13029342 1 1 1 1 0 28 2 | chr7 13029596 13029675 1 1 1 6 0 46 3 | chr7 13029996 13030082 1 1 1 10 0 50 4 | chr7 13030207 13030288 1 1 1 6 0 41 5 | chr7 13030376 13030454 1 1 1 97 0 50 6 | chr7 13030593 13030688 1 1 1 78 0 49 7 | chr7 13032203 13032288 2 2 1 4 0 36 8 | chr7 13032351 13032434 2 2 1 10 0 44 9 | chr7 13032566 13032641 2 2 1 13 0 47 10 | chr7 13032822 13033828 2 2 1 22 0 50 11 | chr7 13034043 13034634 2 2 1 16 0 49 12 | chr7 130164124 130167702 2 2 1 35 2 50 13 | chr7 130164216 130167702 2 2 1 46 2 50 14 | chr7 130167809 130169738 2 2 1 64 0 50 15 | chr7 130169877 130171611 2 2 1 65 1 50 16 | chr7 130171683 130172816 2 2 1 73 0 50 17 | chr7 130172940 130177674 2 2 1 54 1 49 18 | chr7 130177866 130180364 2 2 1 74 0 49 19 | chr7 130180476 130182640 2 2 1 52 0 48 20 | chr7 130182763 130185228 2 2 1 42 0 49 21 | chr7 130185381 130196171 0 0 1 34 0 48 22 | chr7 130195278 130196177 2 2 0 25 0 46 23 | chr7 130196375 130198418 2 2 1 2 0 34 24 | chr7 130196375 130199757 2 2 1 64 0 49 25 | chr7 130199906 130200982 2 2 1 64 0 50 26 | chr7 130201174 130218997 2 2 1 35 0 46 27 | chr7 130219122 130228622 2 2 1 9 0 39 28 | chr7 130228793 130241199 2 2 1 11 0 47 29 | chr7 130241278 130261748 2 2 1 22 0 50 30 | chr7 130262067 130263703 2 2 0 7 0 32 31 | chr7 130394737 130418447 2 2 1 23 0 50 32 | chr7 130418569 130464130 2 2 1 28 0 49 33 | chr7 130464231 130467255 2 2 1 42 0 48 34 | chr7 130467438 130481682 2 2 1 28 0 39 35 | chr7 130481716 130504693 2 2 1 25 0 33 36 | chr7 130504823 130507481 2 2 1 13 0 37 37 | chr7 130539111 130539813 2 2 1 1 0 45 38 | chr7 130542811 130545894 2 2 1 1 0 11 39 | -------------------------------------------------------------------------------- /outrigger/tests/data/treutlein2014/unprocessed/sj_out_tab/SRR1033965_1.polyATrim.adapterTrim.rmRep.bamSJ.out.tab: -------------------------------------------------------------------------------- 1 | chr7 13028555 13028663 1 1 1 64 0 49 2 | chr7 13028779 13028880 1 1 1 86 0 49 3 | chr7 13028988 13029087 1 1 1 109 0 37 4 | chr7 13029125 13029206 1 1 1 161 0 38 5 | chr7 13029253 13029342 1 1 1 165 1 48 6 | chr7 13029596 13029675 1 1 1 181 0 50 7 | chr7 13029996 13030082 1 1 1 324 0 50 8 | chr7 13030207 13030288 1 1 1 297 0 50 9 | chr7 13030376 13030454 1 1 1 303 0 50 10 | chr7 13030593 13030688 1 1 1 327 0 50 11 | chr7 13035755 13035841 2 2 1 1 0 17 12 | chr7 13035906 13036211 2 2 1 1 0 20 13 | chr7 130164124 130167702 2 2 1 1 0 29 14 | chr7 130418569 130464130 2 2 1 2 0 47 15 | chr7 130464231 130467255 2 2 1 3 0 46 16 | chr7 130467438 130481682 2 2 1 1 0 33 17 | chr7 130481716 130503721 2 2 1 1 0 33 18 | chr7 130503851 130507481 2 2 1 1 0 13 19 | chr7 130507700 130509006 2 2 1 20 0 32 20 | chr7 130509259 130510810 2 2 1 94 0 50 21 | chr7 130510915 130513761 2 2 1 116 0 48 22 | chr7 130513825 130516104 2 2 1 116 0 50 23 | chr7 130516169 130519355 2 2 1 83 0 50 24 | chr7 130532693 130533576 2 2 1 18 0 50 25 | chr7 130759326 130759533 1 1 1 20 0 49 26 | chr7 130759641 130759914 1 1 1 19 0 40 27 | chr7 130760036 130764253 1 1 1 8 0 35 28 | -------------------------------------------------------------------------------- /outrigger/tests/data/treutlein2014/unprocessed/sj_out_tab/SRR1033966_1.polyATrim.adapterTrim.rmRep.bamSJ.out.tab: -------------------------------------------------------------------------------- 1 | chr7 13030207 13030288 1 1 1 1 0 50 2 | chr7 13030376 13030454 1 1 1 8 0 46 3 | chr7 13030593 13030688 1 1 1 9 0 38 4 | chr7 13032203 13032288 2 2 1 114 0 50 5 | chr7 13032351 13032434 2 2 1 117 0 50 6 | chr7 13032566 13032641 2 2 1 21 0 43 7 | chr7 13032822 13033828 2 2 1 15 0 50 8 | chr7 13034043 13034634 2 2 1 9 0 50 9 | -------------------------------------------------------------------------------- /outrigger/tests/data/treutlein2014/unprocessed/sj_out_tab/SRR1033967_1.polyATrim.adapterTrim.rmRep.bamSJ.out.tab: -------------------------------------------------------------------------------- 1 | chr7 13030376 13030454 1 1 1 5 0 19 2 | chr7 13030593 13030688 1 1 1 3 0 49 3 | chr7 13032203 13032288 2 2 1 4 0 42 4 | chr7 13032351 13032434 2 2 1 2 0 27 5 | chr7 13032566 13032641 2 2 1 2 0 35 6 | chr7 13032822 13033828 2 2 1 7 0 49 7 | chr7 13034043 13034634 2 2 1 10 0 49 8 | chr7 130509259 130510810 2 2 1 3 0 34 9 | chr7 130510915 130513761 2 2 1 8 0 43 10 | chr7 130513825 130516104 2 2 1 8 0 50 11 | chr7 130516169 130519355 2 2 1 2 0 49 12 | -------------------------------------------------------------------------------- /outrigger/tests/data/treutlein2014/unprocessed/sj_out_tab/SRR1033968_1.polyATrim.adapterTrim.rmRep.bamSJ.out.tab: -------------------------------------------------------------------------------- 1 | chr7 13030593 13030688 1 1 1 2 0 49 2 | chr7 13032203 13032288 2 2 1 51 0 50 3 | chr7 13032351 13032434 2 2 1 57 0 50 4 | chr7 13032566 13032641 2 2 1 56 0 46 5 | chr7 13032822 13033828 2 2 1 48 0 50 6 | chr7 13034043 13034634 2 2 1 19 0 49 7 | chr7 13035755 13035841 2 2 1 18 0 48 8 | chr7 13035906 13036211 2 2 1 17 0 47 9 | chr7 13036316 13036433 2 2 1 19 0 39 10 | chr7 13036473 13036565 2 2 1 13 0 39 11 | chr7 13036661 13037620 2 2 1 8 0 46 12 | chr7 130164124 130167702 2 2 1 69 9 48 13 | chr7 130164216 130167702 2 2 1 68 9 50 14 | chr7 130167809 130169738 2 2 1 95 1 50 15 | chr7 130169877 130171611 2 2 1 56 0 48 16 | chr7 130171683 130172816 2 2 1 44 0 50 17 | chr7 130172940 130177674 2 2 1 17 0 21 18 | chr7 130751911 130753617 1 1 1 1 0 44 19 | chr7 130760036 130764253 1 1 1 1 0 5 20 | -------------------------------------------------------------------------------- /outrigger/tests/data/treutlein2014/unprocessed/sj_out_tab/SRR1033969_1.polyATrim.adapterTrim.rmRep.bamSJ.out.tab: -------------------------------------------------------------------------------- 1 | chr7 13030593 13030688 1 1 1 2 0 49 2 | chr7 13032203 13032288 2 2 1 94 0 48 3 | chr7 13032351 13032434 2 2 1 93 0 50 4 | chr7 13032566 13032641 2 2 1 98 0 50 5 | chr7 13032822 13033828 2 2 1 67 0 50 6 | chr7 13034043 13034634 2 2 1 36 0 49 7 | chr7 130163063 130164156 2 2 0 89 0 50 8 | chr7 130164216 130167702 2 2 1 88 0 50 9 | chr7 130167809 130169738 2 2 1 54 0 39 10 | -------------------------------------------------------------------------------- /outrigger/tests/data/treutlein2014/unprocessed/sj_out_tab/SRR1033970_1.polyATrim.adapterTrim.rmRep.bamSJ.out.tab: -------------------------------------------------------------------------------- 1 | chr7 13025417 13025643 1 1 1 1 0 40 2 | chr7 13029253 13029342 1 1 1 2 0 17 3 | chr7 13029596 13029675 1 1 1 2 0 44 4 | chr7 13029996 13030082 1 1 1 50 0 50 5 | chr7 13030207 13030288 1 1 1 36 0 50 6 | chr7 13030376 13030454 1 1 1 108 0 50 7 | chr7 13030593 13030688 1 1 1 120 0 50 8 | chr7 13032203 13032288 2 2 1 96 0 50 9 | chr7 13032351 13032434 2 2 1 123 0 50 10 | chr7 13032566 13032641 2 2 1 140 0 49 11 | chr7 13032566 13033828 2 2 0 1 0 31 12 | chr7 13032822 13033828 2 2 1 81 0 50 13 | chr7 13034043 13034634 2 2 1 51 0 49 14 | chr7 130164124 130167702 2 2 1 1 3 16 15 | chr7 130164216 130167702 2 2 1 36 3 50 16 | chr7 130167809 130169738 2 2 1 36 1 50 17 | chr7 130169877 130171611 2 2 1 37 0 49 18 | chr7 130171683 130172816 2 2 1 38 1 50 19 | chr7 130172940 130177674 2 2 1 24 0 49 20 | chr7 130177866 130180364 2 2 1 32 0 45 21 | chr7 130180476 130182640 2 2 1 38 0 49 22 | chr7 130182763 130185228 2 2 1 32 0 47 23 | chr7 130185381 130196171 0 0 1 24 0 48 24 | chr7 130196375 130199757 2 2 1 14 0 49 25 | chr7 130199906 130200982 2 2 1 18 0 45 26 | chr7 130201174 130218997 2 2 1 16 0 49 27 | chr7 130219122 130228622 2 2 1 8 0 45 28 | chr7 130228793 130261748 2 2 1 7 0 40 29 | chr7 130262067 130263336 2 2 0 11 0 42 30 | chr7 130263537 130264047 2 2 0 7 0 41 31 | chr7 130509259 130510810 2 2 1 21 0 49 32 | chr7 130510915 130513761 2 2 1 19 0 42 33 | chr7 130513825 130516104 2 2 1 28 0 50 34 | chr7 130516169 130519355 2 2 1 20 0 48 35 | -------------------------------------------------------------------------------- /outrigger/tests/data/treutlein2014/unprocessed/sj_out_tab/SRR1033971_1.polyATrim.adapterTrim.rmRep.bamSJ.out.tab: -------------------------------------------------------------------------------- 1 | chr7 13030207 13030288 1 1 1 1 0 33 2 | chr7 13030593 13030688 1 1 1 1 0 29 3 | chr7 13032203 13032288 2 2 1 34 0 50 4 | chr7 13032351 13032434 2 2 1 29 0 50 5 | chr7 13032566 13032641 2 2 1 28 0 50 6 | chr7 13032822 13033828 2 2 1 22 0 49 7 | chr7 13034043 13034634 2 2 1 10 0 49 8 | chr7 13035755 13035841 2 2 1 1 0 46 9 | chr7 13035906 13036211 2 2 1 1 0 29 10 | chr7 130164124 130167702 2 2 1 100 5 48 11 | chr7 130164216 130167702 2 2 1 22 5 47 12 | chr7 130167809 130169738 2 2 1 141 2 50 13 | chr7 130169877 130171611 2 2 1 130 0 49 14 | chr7 130171683 130172816 2 2 1 142 0 50 15 | chr7 130172940 130177674 2 2 1 124 0 49 16 | chr7 130177866 130180364 2 2 1 118 0 50 17 | chr7 130180476 130182640 2 2 1 94 0 49 18 | chr7 130182763 130185228 2 2 1 78 0 49 19 | chr7 130185381 130196171 0 0 1 85 0 50 20 | chr7 130196375 130199757 2 2 1 29 0 48 21 | chr7 130199906 130200982 2 2 1 27 0 49 22 | chr7 130509259 130510810 2 2 1 11 0 46 23 | chr7 130510915 130513761 2 2 1 14 0 48 24 | chr7 130513825 130516104 2 2 1 33 0 50 25 | chr7 130516169 130519355 2 2 1 30 0 48 26 | chr7 130532693 130533576 2 2 1 2 0 37 27 | chr7 130533667 130533769 2 2 1 3 0 49 28 | chr7 130759326 130759533 1 1 1 25 0 49 29 | chr7 130759641 130759914 1 1 1 30 0 45 30 | chr7 130760036 130764253 1 1 1 28 0 45 31 | -------------------------------------------------------------------------------- /outrigger/tests/data/treutlein2014/unprocessed/sj_out_tab/SRR1033974_1.polyATrim.adapterTrim.rmRep.bamSJ.out.tab: -------------------------------------------------------------------------------- 1 | chr7 13028988 13029087 1 1 1 74 0 50 2 | chr7 13029125 13029206 1 1 1 1 0 3 3 | chr7 13029596 13029675 1 1 1 80 0 50 4 | chr7 13029996 13030082 1 1 1 149 0 50 5 | chr7 13030207 13030288 1 1 1 150 0 50 6 | chr7 13030376 13030454 1 1 1 145 0 50 7 | chr7 13030593 13030688 1 1 1 129 0 50 8 | chr7 13032203 13032288 2 2 1 77 0 50 9 | chr7 13032351 13032434 2 2 1 170 0 50 10 | chr7 13032566 13032641 2 2 1 188 0 50 11 | chr7 13032822 13033828 2 2 1 70 0 49 12 | chr7 13034043 13034634 2 2 1 36 0 49 13 | -------------------------------------------------------------------------------- /outrigger/tests/data/treutlein2014/unprocessed/sj_out_tab/SRR1033976_1.polyATrim.adapterTrim.rmRep.bamSJ.out.tab: -------------------------------------------------------------------------------- 1 | chr7 13027753 13027832 1 1 1 43 0 50 2 | chr7 13027950 13028020 1 1 1 48 0 50 3 | chr7 13028136 13028407 1 1 1 49 0 50 4 | chr7 13028555 13028663 1 1 1 56 0 49 5 | chr7 13028779 13028880 1 1 1 55 0 48 6 | chr7 13028988 13029087 1 1 1 73 0 37 7 | chr7 13029125 13029206 1 1 1 74 0 38 8 | chr7 13029253 13029342 1 1 1 70 0 48 9 | chr7 13029596 13029675 1 1 1 48 0 50 10 | chr7 13029996 13030082 1 1 1 88 0 49 11 | chr7 13030207 13030288 1 1 1 64 0 50 12 | chr7 13030376 13030454 1 1 1 82 0 50 13 | chr7 13030593 13030688 1 1 1 73 0 49 14 | chr7 13032203 13032288 2 2 1 1 0 50 15 | chr7 13032351 13032434 2 2 1 2 0 50 16 | chr7 13032566 13032641 2 2 1 1 0 42 17 | chr7 13032822 13033828 2 2 1 3 0 42 18 | chr7 13034043 13034634 2 2 1 11 0 49 19 | chr7 130164124 130167702 2 2 1 0 2 8 20 | chr7 130164216 130167702 2 2 1 30 2 50 21 | chr7 130167809 130169738 2 2 1 13 0 39 22 | chr7 130532693 130533576 2 2 1 1 0 34 23 | chr7 130533667 130533769 2 2 1 1 0 38 24 | chr7 130533862 130535523 2 2 1 1 0 31 25 | chr7 130535573 130536982 2 2 1 1 0 36 26 | chr7 130759326 130759533 1 1 1 5 0 31 27 | chr7 130759641 130759914 1 1 1 7 0 42 28 | chr7 130760036 130764253 1 1 1 6 0 45 29 | chr7 130962178 130979300 1 1 1 12 0 45 30 | chr7 130979496 130979951 1 1 1 7 0 33 31 | chr7 130979985 130981656 1 1 1 7 0 33 32 | chr7 130981772 130982236 1 1 1 8 0 50 33 | chr7 130982295 130983659 1 1 1 7 0 49 34 | chr7 130983756 130984962 1 1 1 14 0 50 35 | -------------------------------------------------------------------------------- /outrigger/tests/data/treutlein2014/unprocessed/sj_out_tab/SRR1033977_1.polyATrim.adapterTrim.rmRep.bamSJ.out.tab: -------------------------------------------------------------------------------- 1 | chr7 13029996 13030082 1 1 1 1 0 25 2 | chr7 13030376 13030454 1 1 1 4 0 29 3 | chr7 13030593 13030688 1 1 1 7 0 39 4 | chr7 13032203 13032288 2 2 1 28 0 49 5 | chr7 13032351 13032434 2 2 1 37 0 50 6 | chr7 13032566 13032641 2 2 1 30 1 49 7 | chr7 13032822 13033828 2 2 1 15 0 49 8 | chr7 13034039 13034630 2 2 0 1 0 31 9 | chr7 13034043 13034634 2 2 1 25 0 50 10 | chr7 13035755 13035841 2 2 1 17 0 50 11 | chr7 13035906 13036211 2 2 1 11 0 48 12 | chr7 13036316 13036433 2 2 1 6 0 39 13 | chr7 13036473 13036565 2 2 1 5 0 39 14 | chr7 13036661 13037620 2 2 1 2 0 28 15 | chr7 130164124 130167702 2 2 1 0 3 10 16 | chr7 130164216 130167702 2 2 1 35 3 50 17 | chr7 130167809 130169738 2 2 1 41 0 50 18 | chr7 130169877 130171611 2 2 1 34 0 46 19 | chr7 130171683 130172816 2 2 1 35 0 50 20 | chr7 130172940 130177674 2 2 1 27 0 49 21 | chr7 130177866 130180364 2 2 1 30 0 45 22 | chr7 130180476 130182640 2 2 1 19 0 42 23 | chr7 130509259 130510810 2 2 1 8 0 31 24 | chr7 130510915 130513761 2 2 1 14 0 31 25 | chr7 130513825 130516104 2 2 1 16 0 50 26 | chr7 130516169 130519355 2 2 1 4 0 49 27 | chr7 130532693 130533576 2 2 1 2 0 50 28 | chr7 130533862 130535523 2 2 1 1 0 42 29 | chr7 130535573 130536982 2 2 1 2 0 49 30 | chr7 130759326 130759533 1 1 1 1 0 26 31 | chr7 130759641 130759914 1 1 1 1 0 46 32 | -------------------------------------------------------------------------------- /outrigger/tests/data/treutlein2014/unprocessed/sj_out_tab/SRR1033978_1.polyATrim.adapterTrim.rmRep.bamSJ.out.tab: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/YeoLab/outrigger/9da86d2d8d137b309a53cae8851ba867cf757201/outrigger/tests/data/treutlein2014/unprocessed/sj_out_tab/SRR1033978_1.polyATrim.adapterTrim.rmRep.bamSJ.out.tab -------------------------------------------------------------------------------- /outrigger/tests/data/treutlein2014/unprocessed/sj_out_tab/SRR1033979_1.polyATrim.adapterTrim.rmRep.bamSJ.out.tab: -------------------------------------------------------------------------------- 1 | chr7 13030593 13030688 1 1 1 4 0 36 2 | chr7 13032203 13032288 2 2 1 48 0 50 3 | chr7 13032351 13032434 2 2 1 56 0 48 4 | chr7 13032566 13032641 2 2 1 73 0 46 5 | chr7 13032822 13033828 2 2 1 27 0 44 6 | chr7 13034043 13034634 2 2 1 17 0 50 7 | chr7 130180476 130182640 2 2 1 53 0 49 8 | chr7 130742302 130751189 1 1 0 10 0 46 9 | chr7 130751334 130751833 1 1 1 35 0 50 10 | chr7 130751911 130753617 1 1 1 37 0 44 11 | chr7 130753662 130759164 1 1 1 31 0 44 12 | chr7 130759326 130759533 1 1 1 34 0 50 13 | chr7 130759641 130759914 1 1 1 27 0 46 14 | chr7 130760036 130764253 1 1 1 21 0 49 15 | chr7 130865984 130877733 1 1 1 2 0 26 16 | chr7 130877895 130882329 1 1 1 6 0 43 17 | chr7 130882387 130885402 1 1 1 5 0 46 18 | chr7 130885449 130892180 1 1 1 5 0 38 19 | chr7 130892279 130897324 1 1 1 5 0 47 20 | chr7 130897451 130900516 1 1 1 1 0 49 21 | -------------------------------------------------------------------------------- /outrigger/tests/data/treutlein2014/unprocessed/sj_out_tab/SRR1033980_1.polyATrim.adapterTrim.rmRep.bamSJ.out.tab: -------------------------------------------------------------------------------- 1 | chr7 13028988 13029087 1 1 1 5 0 37 2 | chr7 13029125 13029206 1 1 1 5 0 38 3 | chr7 13029253 13029342 1 1 1 4 0 44 4 | chr7 13029596 13029675 1 1 1 9 0 36 5 | chr7 13029996 13030082 1 1 1 8 0 48 6 | chr7 13030207 13030288 1 1 1 17 0 50 7 | chr7 13030376 13030454 1 1 1 25 0 47 8 | chr7 13030593 13030688 1 1 1 32 0 47 9 | chr7 13032203 13032288 2 2 1 67 0 50 10 | chr7 13032351 13032434 2 2 1 72 0 50 11 | chr7 13032566 13032641 2 2 1 86 0 50 12 | chr7 13032822 13033828 2 2 1 48 0 49 13 | chr7 13034043 13034501 2 2 0 4 0 45 14 | chr7 13034043 13034634 2 2 1 30 0 49 15 | chr7 130163063 130167702 2 2 0 14 0 44 16 | chr7 130164124 130167702 2 2 1 0 2 11 17 | chr7 130164216 130167702 2 2 1 36 2 50 18 | chr7 130167809 130169738 2 2 1 21 1 46 19 | chr7 130169877 130171611 2 2 1 24 0 46 20 | chr7 130171683 130172816 2 2 1 18 0 40 21 | chr7 130172940 130177674 2 2 1 16 0 49 22 | chr7 130177866 130180364 2 2 1 26 0 48 23 | chr7 130180476 130182640 2 2 1 15 0 48 24 | chr7 130182763 130185228 2 2 1 6 0 50 25 | chr7 130185381 130196171 0 0 1 3 0 48 26 | chr7 130196375 130199757 2 2 1 11 0 47 27 | chr7 130199906 130200982 2 2 1 8 0 48 28 | chr7 130201174 130218997 2 2 1 6 0 44 29 | chr7 130219122 130228622 2 2 1 3 0 30 30 | chr7 130228793 130241199 2 2 1 6 0 48 31 | chr7 130241278 130242377 2 2 1 12 0 49 32 | chr7 130242645 130261748 2 2 1 2 0 18 33 | chr7 130375018 130375895 2 2 0 6 0 40 34 | chr7 130509259 130510810 2 2 1 1 0 11 35 | chr7 130510915 130513761 2 2 1 1 0 12 36 | chr7 130532693 130533576 2 2 1 3 0 50 37 | chr7 130533667 130533769 2 2 1 2 0 19 38 | chr7 130877895 130882329 1 1 1 1 0 32 39 | chr7 130882387 130885402 1 1 1 1 0 44 40 | -------------------------------------------------------------------------------- /outrigger/tests/data/treutlein2014/unprocessed/sj_out_tab/SRR1033981_1.polyATrim.adapterTrim.rmRep.bamSJ.out.tab: -------------------------------------------------------------------------------- 1 | chr7 13032351 13032434 2 2 1 2 0 11 2 | chr7 13032822 13033828 2 2 1 1 0 38 3 | chr7 130164124 130167702 2 2 1 4 0 41 4 | chr7 130167809 130169738 2 2 1 4 0 37 5 | chr7 130169877 130171611 2 2 1 4 0 44 6 | chr7 130171683 130172816 2 2 1 6 0 46 7 | chr7 130172940 130177674 2 2 1 5 0 49 8 | chr7 130177866 130180364 2 2 1 3 0 43 9 | -------------------------------------------------------------------------------- /outrigger/tests/data/treutlein2014/unprocessed/sj_out_tab/SRR1033982_1.polyATrim.adapterTrim.rmRep.bamSJ.out.tab: -------------------------------------------------------------------------------- 1 | chr7 13032203 13032288 2 2 1 2 0 43 2 | chr7 13032351 13032434 2 2 1 5 0 45 3 | chr7 13032566 13032641 2 2 1 3 0 28 4 | chr7 13032822 13033828 2 2 1 6 0 45 5 | chr7 13034043 13034634 2 2 1 2 0 49 6 | chr7 13035755 13035841 2 2 1 1 0 4 7 | chr7 13035906 13036211 2 2 1 1 0 45 8 | chr7 13036316 13036433 2 2 1 2 0 28 9 | chr7 13036473 13036565 2 2 1 2 0 34 10 | chr7 130003255 130041045 2 2 0 1 0 39 11 | chr7 130759326 130759533 1 1 1 3 0 38 12 | chr7 130759641 130759914 1 1 1 3 0 37 13 | chr7 130760036 130764253 1 1 1 3 0 45 14 | -------------------------------------------------------------------------------- /outrigger/tests/data/treutlein2014/unprocessed/sj_out_tab/SRR1033983_1.polyATrim.adapterTrim.rmRep.bamSJ.out.tab: -------------------------------------------------------------------------------- 1 | chr7 13032203 13032288 2 2 1 1 0 27 2 | chr7 13032351 13032434 2 2 1 1 0 50 3 | -------------------------------------------------------------------------------- /outrigger/tests/data/treutlein2014/unprocessed/sj_out_tab/SRR1033984_1.polyATrim.adapterTrim.rmRep.bamSJ.out.tab: -------------------------------------------------------------------------------- 1 | chr7 13032351 13032434 2 2 1 2 0 34 2 | chr7 13032566 13032641 2 2 1 2 0 35 3 | chr7 13032822 13033828 2 2 1 1 0 38 4 | -------------------------------------------------------------------------------- /outrigger/tests/data/treutlein2014/unprocessed/sj_out_tab/SRR1033985_1.polyATrim.adapterTrim.rmRep.bamSJ.out.tab: -------------------------------------------------------------------------------- 1 | chr7 13032351 13032434 2 2 1 1 0 19 2 | chr7 13036316 13036433 2 2 1 1 0 17 3 | -------------------------------------------------------------------------------- /outrigger/tests/data/treutlein2014/unprocessed/sj_out_tab/SRR1033986_1.polyATrim.adapterTrim.rmRep.bamSJ.out.tab: -------------------------------------------------------------------------------- 1 | chr7 13032203 13032288 2 2 1 1 0 13 2 | chr7 13032351 13032434 2 2 1 3 0 42 3 | chr7 13032566 13032641 2 2 1 2 0 45 4 | chr7 13032822 13033828 2 2 1 2 0 15 5 | chr7 13034043 13034634 2 2 1 1 0 23 6 | -------------------------------------------------------------------------------- /outrigger/tests/data/treutlein2014/unprocessed/sj_out_tab/SRR1033987_1.polyATrim.adapterTrim.rmRep.bamSJ.out.tab: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/YeoLab/outrigger/9da86d2d8d137b309a53cae8851ba867cf757201/outrigger/tests/data/treutlein2014/unprocessed/sj_out_tab/SRR1033987_1.polyATrim.adapterTrim.rmRep.bamSJ.out.tab -------------------------------------------------------------------------------- /outrigger/tests/data/treutlein2014/unprocessed/sj_out_tab/SRR1033988_1.polyATrim.adapterTrim.rmRep.bamSJ.out.tab: -------------------------------------------------------------------------------- 1 | chr7 13032203 13032288 2 2 1 1 0 36 2 | chr7 13032351 13032434 2 2 1 1 0 17 3 | -------------------------------------------------------------------------------- /outrigger/tests/data/treutlein2014/unprocessed/sj_out_tab/SRR1033989_1.polyATrim.adapterTrim.rmRep.bamSJ.out.tab: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/YeoLab/outrigger/9da86d2d8d137b309a53cae8851ba867cf757201/outrigger/tests/data/treutlein2014/unprocessed/sj_out_tab/SRR1033989_1.polyATrim.adapterTrim.rmRep.bamSJ.out.tab -------------------------------------------------------------------------------- /outrigger/tests/data/treutlein2014/unprocessed/sj_out_tab/SRR1033990_1.polyATrim.adapterTrim.rmRep.bamSJ.out.tab: -------------------------------------------------------------------------------- 1 | chr7 13032351 13032434 2 2 1 2 0 36 2 | chr7 13032566 13032641 2 2 1 1 0 35 3 | chr7 130164124 130167702 2 2 1 4 0 37 4 | chr7 130167809 130169738 2 2 1 5 0 39 5 | -------------------------------------------------------------------------------- /outrigger/tests/data/treutlein2014/unprocessed/sj_out_tab/SRR1033991_1.polyATrim.adapterTrim.rmRep.bamSJ.out.tab: -------------------------------------------------------------------------------- 1 | chr7 130164216 130167702 2 2 1 8 0 31 2 | -------------------------------------------------------------------------------- /outrigger/tests/data/treutlein2014/unprocessed/sj_out_tab/SRR1033992_1.polyATrim.adapterTrim.rmRep.bamSJ.out.tab: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/YeoLab/outrigger/9da86d2d8d137b309a53cae8851ba867cf757201/outrigger/tests/data/treutlein2014/unprocessed/sj_out_tab/SRR1033992_1.polyATrim.adapterTrim.rmRep.bamSJ.out.tab -------------------------------------------------------------------------------- /outrigger/tests/data/treutlein2014/unprocessed/sj_out_tab/SRR1033993_1.polyATrim.adapterTrim.rmRep.bamSJ.out.tab: -------------------------------------------------------------------------------- 1 | chr7 130164124 130167702 2 2 1 1 0 29 2 | chr7 130171683 130172816 2 2 1 2 0 40 3 | chr7 130510915 130513761 2 2 1 1 0 19 4 | -------------------------------------------------------------------------------- /outrigger/tests/data/treutlein2014/unprocessed/sj_out_tab/SRR1033994_1.polyATrim.adapterTrim.rmRep.bamSJ.out.tab: -------------------------------------------------------------------------------- 1 | chr7 13032203 13032288 2 2 1 1 0 28 2 | chr7 13032351 13032434 2 2 1 4 0 50 3 | chr7 13032566 13032641 2 2 1 3 0 44 4 | chr7 13032822 13033828 2 2 1 2 0 10 5 | chr7 130509259 130510810 2 2 1 1 0 27 6 | chr7 130510915 130513761 2 2 1 1 0 33 7 | chr7 130513825 130516104 2 2 1 2 0 29 8 | chr7 130516169 130519355 2 2 1 3 0 47 9 | chr7 130885449 130892180 1 1 1 1 0 34 10 | -------------------------------------------------------------------------------- /outrigger/tests/data/treutlein2014/unprocessed/sj_out_tab/SRR1033995_1.polyATrim.adapterTrim.rmRep.bamSJ.out.tab: -------------------------------------------------------------------------------- 1 | chr7 13029996 13030082 1 1 1 7 0 46 2 | chr7 13030376 13030454 1 1 1 1 0 26 3 | chr7 13030593 13030688 1 1 1 5 0 41 4 | chr7 13032822 13033828 2 2 1 1 0 5 5 | -------------------------------------------------------------------------------- /outrigger/tests/data/treutlein2014/unprocessed/sj_out_tab/SRR1033996_1.polyATrim.adapterTrim.rmRep.bamSJ.out.tab: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/YeoLab/outrigger/9da86d2d8d137b309a53cae8851ba867cf757201/outrigger/tests/data/treutlein2014/unprocessed/sj_out_tab/SRR1033996_1.polyATrim.adapterTrim.rmRep.bamSJ.out.tab -------------------------------------------------------------------------------- /outrigger/tests/data/treutlein2014/unprocessed/sj_out_tab/SRR1033997_1.polyATrim.adapterTrim.rmRep.bamSJ.out.tab: -------------------------------------------------------------------------------- 1 | chr7 13029125 13029206 1 1 1 3 0 38 2 | chr7 13029253 13029342 1 1 1 6 0 40 3 | chr7 13029996 13030082 1 1 1 3 0 40 4 | chr7 13030207 13030288 1 1 1 1 0 10 5 | chr7 13030376 13030454 1 1 1 5 0 49 6 | chr7 13030593 13030688 1 1 1 4 0 26 7 | -------------------------------------------------------------------------------- /outrigger/tests/data/treutlein2014/unprocessed/sj_out_tab/SRR1033998_1.polyATrim.adapterTrim.rmRep.bamSJ.out.tab: -------------------------------------------------------------------------------- 1 | chr7 13032203 13032288 2 2 1 2 0 26 2 | chr7 13032351 13032434 2 2 1 7 0 27 3 | chr7 13032566 13032641 2 2 1 2 0 49 4 | chr7 13032822 13033828 2 2 1 2 0 50 5 | chr7 130509259 130510810 2 2 1 15 0 46 6 | chr7 130510915 130513761 2 2 1 26 0 49 7 | -------------------------------------------------------------------------------- /outrigger/tests/data/treutlein2014/unprocessed/sj_out_tab/SRR1033999_1.polyATrim.adapterTrim.rmRep.bamSJ.out.tab: -------------------------------------------------------------------------------- 1 | chr7 13032351 13032434 2 2 1 1 0 48 2 | chr7 13032566 13033828 2 2 0 1 0 43 3 | chr7 13032822 13033828 2 2 1 1 0 12 4 | chr7 13034043 13034634 2 2 1 1 0 30 5 | -------------------------------------------------------------------------------- /outrigger/tests/data/treutlein2014/unprocessed/sj_out_tab/SRR1034000_1.polyATrim.adapterTrim.rmRep.bamSJ.out.tab: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/YeoLab/outrigger/9da86d2d8d137b309a53cae8851ba867cf757201/outrigger/tests/data/treutlein2014/unprocessed/sj_out_tab/SRR1034000_1.polyATrim.adapterTrim.rmRep.bamSJ.out.tab -------------------------------------------------------------------------------- /outrigger/tests/data/treutlein2014/unprocessed/sj_out_tab/SRR1034001_1.polyATrim.adapterTrim.rmRep.bamSJ.out.tab: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/YeoLab/outrigger/9da86d2d8d137b309a53cae8851ba867cf757201/outrigger/tests/data/treutlein2014/unprocessed/sj_out_tab/SRR1034001_1.polyATrim.adapterTrim.rmRep.bamSJ.out.tab -------------------------------------------------------------------------------- /outrigger/tests/data/treutlein2014/unprocessed/sj_out_tab/SRR1034002_1.polyATrim.adapterTrim.rmRep.bamSJ.out.tab: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/YeoLab/outrigger/9da86d2d8d137b309a53cae8851ba867cf757201/outrigger/tests/data/treutlein2014/unprocessed/sj_out_tab/SRR1034002_1.polyATrim.adapterTrim.rmRep.bamSJ.out.tab -------------------------------------------------------------------------------- /outrigger/tests/data/treutlein2014/unprocessed/sj_out_tab/SRR1034003_1.polyATrim.adapterTrim.rmRep.bamSJ.out.tab: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/YeoLab/outrigger/9da86d2d8d137b309a53cae8851ba867cf757201/outrigger/tests/data/treutlein2014/unprocessed/sj_out_tab/SRR1034003_1.polyATrim.adapterTrim.rmRep.bamSJ.out.tab -------------------------------------------------------------------------------- /outrigger/tests/data/treutlein2014/unprocessed/sj_out_tab/SRR1034004_1.polyATrim.adapterTrim.rmRep.bamSJ.out.tab: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/YeoLab/outrigger/9da86d2d8d137b309a53cae8851ba867cf757201/outrigger/tests/data/treutlein2014/unprocessed/sj_out_tab/SRR1034004_1.polyATrim.adapterTrim.rmRep.bamSJ.out.tab -------------------------------------------------------------------------------- /outrigger/tests/data/treutlein2014/unprocessed/sj_out_tab/SRR1034005_1.polyATrim.adapterTrim.rmRep.bamSJ.out.tab: -------------------------------------------------------------------------------- 1 | chr7 130167809 130169738 2 2 1 9 0 41 2 | chr7 130169877 130171611 2 2 1 3 0 45 3 | chr7 130171683 130172816 2 2 1 5 0 34 4 | chr7 130172940 130177674 2 2 1 1 0 22 5 | chr7 130759326 130759533 1 1 1 2 0 32 6 | -------------------------------------------------------------------------------- /outrigger/tests/data/treutlein2014/unprocessed/sj_out_tab/SRR1034006_1.polyATrim.adapterTrim.rmRep.bamSJ.out.tab: -------------------------------------------------------------------------------- 1 | chr7 13032351 13032434 2 2 1 1 0 35 2 | -------------------------------------------------------------------------------- /outrigger/tests/data/treutlein2014/unprocessed/sj_out_tab/SRR1034007_1.polyATrim.adapterTrim.rmRep.bamSJ.out.tab: -------------------------------------------------------------------------------- 1 | chr7 13032566 13032641 2 2 1 3 0 30 2 | chr7 13032822 13033828 2 2 1 1 0 13 3 | chr7 130877895 130882329 1 1 1 2 0 43 4 | chr7 130882387 130885402 1 1 1 1 0 11 5 | chr7 130900661 130902176 1 1 1 1 0 47 6 | chr7 130902246 130904869 1 1 1 1 0 30 7 | chr7 130904935 130905390 1 1 1 1 0 6 8 | -------------------------------------------------------------------------------- /outrigger/tests/data/treutlein2014/unprocessed/sj_out_tab/SRR1034008_1.polyATrim.adapterTrim.rmRep.bamSJ.out.tab: -------------------------------------------------------------------------------- 1 | chr7 13032203 13032288 2 2 1 11 0 36 2 | chr7 13032351 13032434 2 2 1 32 0 50 3 | chr7 13032566 13032641 2 2 1 31 0 49 4 | chr7 13032822 13033828 2 2 1 10 0 49 5 | chr7 13034043 13034634 2 2 1 4 0 45 6 | chr7 130164124 130167702 2 2 1 12 0 42 7 | chr7 130167809 130169738 2 2 1 6 0 50 8 | chr7 130169877 130171611 2 2 1 16 0 48 9 | chr7 130171683 130172816 2 2 1 11 0 45 10 | chr7 130172940 130177674 2 2 1 11 0 49 11 | chr7 130177866 130180364 2 2 1 7 0 31 12 | chr7 130180476 130182640 2 2 1 7 0 49 13 | chr7 130182763 130185228 2 2 1 6 0 48 14 | -------------------------------------------------------------------------------- /outrigger/tests/data/treutlein2014/unprocessed/sj_out_tab/SRR1034009_1.polyATrim.adapterTrim.rmRep.bamSJ.out.tab: -------------------------------------------------------------------------------- 1 | chr7 13032203 13032288 2 2 1 2 0 45 2 | chr7 13032351 13032434 2 2 1 3 0 16 3 | chr7 13032566 13032641 2 2 1 3 0 32 4 | chr7 13032822 13033828 2 2 1 3 0 31 5 | chr7 13034043 13034634 2 2 1 1 0 44 6 | chr7 130164216 130167702 2 2 1 5 0 44 7 | chr7 130167809 130169738 2 2 1 3 0 39 8 | chr7 130169877 130171611 2 2 1 1 0 26 9 | chr7 130171683 130172816 2 2 1 1 0 4 10 | chr7 130908426 130909587 1 1 1 1 0 29 11 | chr7 130909804 130910831 1 1 0 2 0 31 12 | -------------------------------------------------------------------------------- /outrigger/tests/data/treutlein2014/unprocessed/sj_out_tab/SRR1034010_1.polyATrim.adapterTrim.rmRep.bamSJ.out.tab: -------------------------------------------------------------------------------- 1 | chr7 13032203 13032288 2 2 1 8 0 49 2 | chr7 13032351 13032434 2 2 1 25 0 48 3 | chr7 13032566 13032641 2 2 1 15 0 45 4 | chr7 13032822 13033828 2 2 1 19 0 48 5 | chr7 13034043 13034501 2 2 0 1 0 21 6 | chr7 13034043 13034634 2 2 1 7 0 49 7 | chr7 130164124 130167702 2 2 1 6 0 46 8 | chr7 130164216 130167702 2 2 1 3 0 39 9 | chr7 130167809 130169738 2 2 1 10 0 46 10 | chr7 130169877 130171611 2 2 1 6 0 45 11 | chr7 130171683 130172816 2 2 1 4 0 39 12 | chr7 130172940 130177674 2 2 1 2 0 25 13 | chr7 130177866 130180364 2 2 1 1 0 35 14 | chr7 130199906 130200982 2 2 1 1 0 15 15 | -------------------------------------------------------------------------------- /outrigger/tests/data/treutlein2014/unprocessed/sj_out_tab/SRR1034011_1.polyATrim.adapterTrim.rmRep.bamSJ.out.tab: -------------------------------------------------------------------------------- 1 | chr7 13034043 13034634 2 2 1 2 0 34 2 | -------------------------------------------------------------------------------- /outrigger/tests/data/treutlein2014/unprocessed/sj_out_tab/SRR1034012_1.polyATrim.adapterTrim.rmRep.bamSJ.out.tab: -------------------------------------------------------------------------------- 1 | chr7 13032203 13032288 2 2 1 5 0 36 2 | chr7 13032351 13032434 2 2 1 6 0 28 3 | chr7 13032566 13032641 2 2 1 4 0 39 4 | chr7 13032822 13033828 2 2 1 2 0 38 5 | -------------------------------------------------------------------------------- /outrigger/tests/data/treutlein2014/unprocessed/sj_out_tab/SRR1034013_1.polyATrim.adapterTrim.rmRep.bamSJ.out.tab: -------------------------------------------------------------------------------- 1 | chr7 130164124 130167702 2 2 1 2 0 15 2 | chr7 130167809 130169738 2 2 1 1 0 39 3 | -------------------------------------------------------------------------------- /outrigger/tests/data/treutlein2014/unprocessed/sj_out_tab/SRR1034014_1.polyATrim.adapterTrim.rmRep.bamSJ.out.tab: -------------------------------------------------------------------------------- 1 | chr7 13032203 13032288 2 2 1 1 0 44 2 | -------------------------------------------------------------------------------- /outrigger/tests/data/treutlein2014/unprocessed/sj_out_tab/SRR1034015_1.polyATrim.adapterTrim.rmRep.bamSJ.out.tab: -------------------------------------------------------------------------------- 1 | chr7 13032203 13032288 2 2 1 1 0 12 2 | chr7 13032351 13032434 2 2 1 1 0 27 3 | chr7 13032566 13032641 2 2 1 1 0 46 4 | chr7 13032822 13033828 2 2 1 1 0 37 5 | -------------------------------------------------------------------------------- /outrigger/tests/data/treutlein2014/unprocessed/sj_out_tab/SRR1034016_1.polyATrim.adapterTrim.rmRep.bamSJ.out.tab: -------------------------------------------------------------------------------- 1 | chr7 130164124 130167702 2 2 1 2 0 41 2 | -------------------------------------------------------------------------------- /outrigger/tests/data/treutlein2014/unprocessed/sj_out_tab/SRR1034017_1.polyATrim.adapterTrim.rmRep.bamSJ.out.tab: -------------------------------------------------------------------------------- 1 | chr7 13032203 13032288 2 2 1 1 0 3 2 | chr7 13032351 13032434 2 2 1 1 0 36 3 | chr7 130164124 130167702 2 2 1 2 2 43 4 | chr7 130164216 130167702 2 2 1 0 2 10 5 | chr7 130167809 130169738 2 2 1 2 0 39 6 | -------------------------------------------------------------------------------- /outrigger/tests/data/treutlein2014/unprocessed/sj_out_tab/SRR1034018_1.polyATrim.adapterTrim.rmRep.bamSJ.out.tab: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/YeoLab/outrigger/9da86d2d8d137b309a53cae8851ba867cf757201/outrigger/tests/data/treutlein2014/unprocessed/sj_out_tab/SRR1034018_1.polyATrim.adapterTrim.rmRep.bamSJ.out.tab -------------------------------------------------------------------------------- /outrigger/tests/data/treutlein2014/unprocessed/sj_out_tab/SRR1034019_1.polyATrim.adapterTrim.rmRep.bamSJ.out.tab: -------------------------------------------------------------------------------- 1 | chr7 13030376 13030454 1 1 1 4 0 45 2 | chr7 13030593 13030688 1 1 1 3 0 41 3 | chr7 130164216 130167702 2 2 1 4 0 31 4 | -------------------------------------------------------------------------------- /outrigger/tests/data/treutlein2014/unprocessed/sj_out_tab/SRR1034020_1.polyATrim.adapterTrim.rmRep.bamSJ.out.tab: -------------------------------------------------------------------------------- 1 | chr7 130241278 130242377 2 2 1 4 0 42 2 | -------------------------------------------------------------------------------- /outrigger/tests/data/treutlein2014/unprocessed/sj_out_tab/SRR1034021_1.polyATrim.adapterTrim.rmRep.bamSJ.out.tab: -------------------------------------------------------------------------------- 1 | chr7 13032566 13032641 2 2 1 2 0 31 2 | chr7 130892279 130897324 1 1 1 7 0 47 3 | chr7 130897451 130900516 1 1 1 6 0 49 4 | chr7 130900661 130902176 1 1 1 3 0 44 5 | chr7 130902246 130904869 1 1 1 8 0 47 6 | chr7 130904935 130905390 1 1 1 4 0 21 7 | chr7 130905455 130908335 1 1 1 3 0 27 8 | -------------------------------------------------------------------------------- /outrigger/tests/data/treutlein2014/unprocessed/sj_out_tab/SRR1034022_1.polyATrim.adapterTrim.rmRep.bamSJ.out.tab: -------------------------------------------------------------------------------- 1 | chr7 130167809 130169738 2 2 1 1 0 32 2 | -------------------------------------------------------------------------------- /outrigger/tests/data/treutlein2014/unprocessed/sj_out_tab/SRR1034023_1.polyATrim.adapterTrim.rmRep.bamSJ.out.tab: -------------------------------------------------------------------------------- 1 | chr7 130164124 130167702 2 2 1 3 0 16 2 | chr7 130167809 130169738 2 2 1 1 0 24 3 | -------------------------------------------------------------------------------- /outrigger/tests/data/treutlein2014/unprocessed/sj_out_tab/SRR1034024_1.polyATrim.adapterTrim.rmRep.bamSJ.out.tab: -------------------------------------------------------------------------------- 1 | chr7 13032351 13032434 2 2 1 1 0 36 2 | chr7 13032566 13032641 2 2 1 2 0 27 3 | chr7 13032822 13033828 2 2 1 2 0 24 4 | chr7 13034043 13034634 2 2 1 2 0 31 5 | -------------------------------------------------------------------------------- /outrigger/tests/data/treutlein2014/unprocessed/sj_out_tab/SRR1034025_1.polyATrim.adapterTrim.rmRep.bamSJ.out.tab: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/YeoLab/outrigger/9da86d2d8d137b309a53cae8851ba867cf757201/outrigger/tests/data/treutlein2014/unprocessed/sj_out_tab/SRR1034025_1.polyATrim.adapterTrim.rmRep.bamSJ.out.tab -------------------------------------------------------------------------------- /outrigger/tests/data/treutlein2014/unprocessed/sj_out_tab/SRR1034026_1.polyATrim.adapterTrim.rmRep.bamSJ.out.tab: -------------------------------------------------------------------------------- 1 | chr7 130164124 130167702 2 2 1 3 0 45 2 | chr7 130167809 130169738 2 2 1 3 0 31 3 | chr7 130169877 130171611 2 2 1 1 0 39 4 | -------------------------------------------------------------------------------- /outrigger/tests/data/treutlein2014/unprocessed/sj_out_tab/SRR1034027_1.polyATrim.adapterTrim.rmRep.bamSJ.out.tab: -------------------------------------------------------------------------------- 1 | chr7 13028136 13028407 1 1 1 7 0 62 2 | chr7 13028555 13028663 1 1 1 12 0 61 3 | chr7 13028779 13028880 1 1 1 15 0 69 4 | chr7 13028988 13029087 1 1 1 14 0 37 5 | chr7 13029125 13029206 1 1 1 15 0 38 6 | chr7 13029253 13029342 1 1 1 21 0 46 7 | chr7 13029596 13029675 1 1 1 15 0 75 8 | chr7 13029996 13030082 1 1 1 8 0 68 9 | chr7 13030207 13030288 1 1 1 16 0 70 10 | chr7 13030376 13030454 1 1 1 9 0 72 11 | chr7 13030593 13030688 1 1 1 12 0 75 12 | chr7 130164124 130167702 2 2 1 2 0 47 13 | chr7 130164216 130167702 2 2 1 6 0 54 14 | chr7 130167809 130169738 2 2 1 2 0 74 15 | chr7 130169877 130171611 2 2 1 6 0 57 16 | chr7 130171683 130172816 2 2 1 8 0 66 17 | chr7 130172940 130177674 2 2 1 7 0 75 18 | chr7 130177866 130180364 2 2 1 6 0 72 19 | chr7 130180476 130182640 2 2 1 3 0 41 20 | chr7 130182763 130185228 2 2 1 8 0 69 21 | chr7 130185381 130196171 0 0 1 4 0 58 22 | chr7 130196375 130199757 2 2 1 7 0 75 23 | chr7 130199906 130200982 2 2 1 6 0 75 24 | chr7 130201174 130218997 2 2 1 9 0 74 25 | chr7 130219122 130228622 2 2 1 4 0 46 26 | chr7 130228793 130261748 2 2 1 7 0 75 27 | chr7 130241278 130242377 2 2 1 9 0 75 28 | chr7 130262067 130265793 2 2 1 4 0 56 29 | chr7 130532693 130533576 2 2 1 1 0 49 30 | chr7 130533667 130533769 2 2 1 2 0 12 31 | chr7 130533862 130535523 2 2 1 3 0 49 32 | chr7 130535573 130536982 2 2 1 3 0 33 33 | chr7 130537078 130538161 2 2 1 4 0 55 34 | chr7 130538253 130539010 2 2 1 2 0 37 35 | chr7 130539111 130539813 2 2 1 3 0 37 36 | chr7 130539966 130542679 2 2 1 4 0 59 37 | chr7 130542811 130545894 2 2 1 2 0 54 38 | chr7 130545973 130546991 2 2 1 1 0 19 39 | -------------------------------------------------------------------------------- /outrigger/tests/data/treutlein2014/unprocessed/sj_out_tab/SRR1034028_1.polyATrim.adapterTrim.rmRep.bamSJ.out.tab: -------------------------------------------------------------------------------- 1 | chr7 13032203 13032288 2 2 1 27 0 62 2 | chr7 13032351 13032434 2 2 1 33 0 62 3 | chr7 13032566 13032641 2 2 1 35 1 72 4 | chr7 13032822 13033828 2 2 1 23 0 63 5 | chr7 13034043 13034634 2 2 1 14 0 66 6 | chr7 130532693 130533576 2 2 1 1 0 54 7 | chr7 130684891 130684985 1 1 0 0 1 33 8 | chr7 130684891 130685208 1 1 0 0 1 40 9 | chr7 130685050 130685208 1 1 0 0 1 40 10 | chr7 130685114 130685208 1 1 0 0 1 40 11 | chr7 130685178 130685271 1 1 0 0 1 50 12 | chr7 130685178 130685584 1 1 0 0 1 50 13 | chr7 130685209 130685458 1 1 0 0 1 25 14 | chr7 130685272 130685333 1 1 0 0 1 31 15 | chr7 130685272 130685395 1 1 0 0 6 72 16 | chr7 130685303 130685364 1 1 0 0 1 46 17 | chr7 130685303 130685426 1 1 0 0 1 26 18 | chr7 130685303 130685489 1 1 0 0 1 26 19 | chr7 130685303 130685552 1 1 0 0 1 26 20 | chr7 130685303 130685584 1 1 0 0 1 20 21 | chr7 130685365 130685615 1 1 0 0 1 31 22 | chr7 130685396 130685521 1 1 0 0 1 42 23 | chr7 130685490 130685615 1 1 0 0 1 64 24 | chr7 130685553 130685615 1 1 0 0 1 64 25 | chr7 130685585 130685615 1 1 0 0 4 46 26 | -------------------------------------------------------------------------------- /outrigger/tests/data/treutlein2014/unprocessed/sj_out_tab/SRR1034029_1.polyATrim.adapterTrim.rmRep.bamSJ.out.tab: -------------------------------------------------------------------------------- 1 | chr7 13032566 13032641 2 2 1 1 0 64 2 | chr7 130510915 130513761 2 2 1 1 0 63 3 | chr7 130513825 130516104 2 2 1 1 0 63 4 | chr7 130516169 130519355 2 2 1 1 0 8 5 | -------------------------------------------------------------------------------- /outrigger/tests/data/treutlein2014/unprocessed/sj_out_tab/SRR1034030_1.polyATrim.adapterTrim.rmRep.bamSJ.out.tab: -------------------------------------------------------------------------------- 1 | chr7 13032203 13032288 2 2 1 7 0 62 2 | chr7 13032351 13032434 2 2 1 10 0 62 3 | chr7 13032566 13032641 2 2 1 9 0 74 4 | chr7 13032822 13033828 2 2 1 7 1 70 5 | chr7 13034043 13034634 2 2 1 6 0 72 6 | chr7 130180476 130182640 2 2 1 5 0 74 7 | chr7 130185381 130196177 2 2 1 1 0 38 8 | chr7 130509259 130510810 2 2 1 1 0 40 9 | chr7 130510915 130513761 2 2 1 3 0 73 10 | chr7 130532693 130533576 2 2 1 5 0 54 11 | chr7 130533667 130533769 2 2 1 5 0 53 12 | chr7 130533862 130535523 2 2 1 5 0 49 13 | chr7 130535573 130536982 2 2 1 4 0 49 14 | chr7 130537078 130538161 2 2 1 1 0 39 15 | chr7 130892279 130897324 1 1 1 1 0 64 16 | chr7 130900661 130902176 1 1 1 1 0 47 17 | chr7 130902246 130904869 1 1 1 1 0 35 18 | -------------------------------------------------------------------------------- /outrigger/tests/data/treutlein2014/unprocessed/sj_out_tab/SRR1034031_1.polyATrim.adapterTrim.rmRep.bamSJ.out.tab: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/YeoLab/outrigger/9da86d2d8d137b309a53cae8851ba867cf757201/outrigger/tests/data/treutlein2014/unprocessed/sj_out_tab/SRR1034031_1.polyATrim.adapterTrim.rmRep.bamSJ.out.tab -------------------------------------------------------------------------------- /outrigger/tests/data/treutlein2014/unprocessed/sj_out_tab/SRR1034032_1.polyATrim.adapterTrim.rmRep.bamSJ.out.tab: -------------------------------------------------------------------------------- 1 | chr7 13035755 13035841 2 2 1 1 0 13 2 | chr7 13035906 13036211 2 2 1 1 0 64 3 | chr7 130716840 130728522 1 1 1 1 0 26 4 | chr7 130729829 130733505 1 1 0 1 0 61 5 | chr7 130733567 130734948 1 1 1 2 0 61 6 | chr7 130735151 130739811 1 1 1 2 0 48 7 | chr7 130739874 130740839 1 1 1 1 0 41 8 | -------------------------------------------------------------------------------- /outrigger/tests/data/treutlein2014/unprocessed/sj_out_tab/SRR1034033_1.polyATrim.adapterTrim.rmRep.bamSJ.out.tab: -------------------------------------------------------------------------------- 1 | chr7 13028779 13028880 1 1 1 5 0 18 2 | chr7 13028988 13029087 1 1 1 10 0 37 3 | chr7 13029125 13029206 1 1 1 11 0 37 4 | chr7 13029253 13029342 1 1 1 13 0 46 5 | chr7 13029596 13029675 1 1 1 10 0 70 6 | chr7 13029996 13030082 1 1 1 13 0 72 7 | chr7 13030207 13030288 1 1 1 19 0 72 8 | chr7 13030376 13030454 1 1 1 18 0 75 9 | chr7 13030593 13030688 1 1 1 18 0 72 10 | chr7 130164216 130167702 2 2 1 10 0 50 11 | chr7 130167809 130169738 2 2 1 8 0 65 12 | chr7 130169877 130171611 2 2 1 7 0 58 13 | chr7 130171683 130172816 2 2 1 6 0 61 14 | chr7 130172940 130177674 2 2 1 5 0 65 15 | chr7 130177866 130180364 2 2 1 6 0 43 16 | chr7 130180476 130182640 2 2 1 7 0 65 17 | chr7 130182763 130185228 2 2 1 3 0 48 18 | -------------------------------------------------------------------------------- /outrigger/tests/data/treutlein2014/unprocessed/sj_out_tab/SRR1034034_1.polyATrim.adapterTrim.rmRep.bamSJ.out.tab: -------------------------------------------------------------------------------- 1 | chr7 13025417 13025643 1 1 1 3 0 73 2 | chr7 13025777 13027616 1 1 1 9 0 60 3 | chr7 13027753 13027832 1 1 1 6 0 74 4 | chr7 13027950 13028020 1 1 1 10 0 72 5 | chr7 13028136 13028407 1 1 1 5 0 73 6 | chr7 13028555 13028663 1 1 1 4 0 73 7 | chr7 13028779 13028880 1 1 1 2 0 67 8 | chr7 13028988 13029087 1 1 1 8 0 37 9 | chr7 13029125 13029206 1 1 1 8 0 37 10 | chr7 13029253 13029342 1 1 1 7 0 46 11 | chr7 13029596 13029675 1 1 1 5 0 64 12 | chr7 13029996 13030082 1 1 1 5 0 49 13 | chr7 13030207 13030288 1 1 1 5 0 70 14 | chr7 13030376 13030454 1 1 1 5 0 72 15 | chr7 13030593 13030688 1 1 1 6 0 62 16 | chr7 13032203 13032288 2 2 1 12 0 63 17 | chr7 13032351 13032434 2 2 1 6 0 62 18 | chr7 13035755 13035841 2 2 1 1 0 32 19 | chr7 130164124 130167702 2 2 1 4 0 46 20 | chr7 130167809 130169738 2 2 1 10 0 56 21 | chr7 130169877 130171611 2 2 1 8 0 70 22 | chr7 130171683 130172816 2 2 1 3 0 61 23 | chr7 130172940 130177674 2 2 1 4 0 68 24 | chr7 130177866 130180364 2 2 1 5 0 61 25 | chr7 130180476 130182640 2 2 1 6 0 74 26 | chr7 130182763 130185228 2 2 1 6 0 64 27 | chr7 130185381 130196171 0 0 1 5 0 45 28 | chr7 130196375 130199757 2 2 1 5 0 72 29 | chr7 130394737 130418447 2 2 1 7 0 71 30 | chr7 130418569 130464130 2 2 1 3 0 71 31 | chr7 130464231 130467255 2 2 1 4 0 73 32 | chr7 130467438 130481682 2 2 1 4 0 33 33 | chr7 130481716 130503721 2 2 1 4 0 33 34 | chr7 130503851 130507481 2 2 1 7 0 59 35 | chr7 130507700 130509006 2 2 1 3 0 69 36 | -------------------------------------------------------------------------------- /outrigger/tests/data/treutlein2014/unprocessed/sj_out_tab/SRR1034035_1.polyATrim.adapterTrim.rmRep.bamSJ.out.tab: -------------------------------------------------------------------------------- 1 | chr7 13032203 13032288 2 2 1 41 0 64 2 | chr7 13032351 13032434 2 2 1 50 0 62 3 | chr7 13032566 13032641 2 2 1 46 0 73 4 | chr7 13032822 13033828 2 2 1 48 0 75 5 | chr7 13034043 13034634 2 2 1 20 0 73 6 | -------------------------------------------------------------------------------- /outrigger/tests/data/treutlein2014/unprocessed/sj_out_tab/SRR1034036_1.polyATrim.adapterTrim.rmRep.bamSJ.out.tab: -------------------------------------------------------------------------------- 1 | chr7 13025062 13025303 1 1 1 1 0 75 2 | chr7 13025417 13025643 1 1 1 3 0 71 3 | chr7 13025777 13027616 1 1 1 1 0 43 4 | chr7 13027753 13027832 1 1 1 1 0 52 5 | chr7 13028136 13028407 1 1 1 12 0 7 6 | chr7 13028555 13028663 1 1 1 21 0 70 7 | chr7 13028779 13028880 1 1 1 23 0 73 8 | chr7 13028988 13029087 1 1 1 27 0 37 9 | chr7 13029125 13029206 1 1 1 25 0 39 10 | chr7 13029253 13029342 1 1 1 24 0 47 11 | chr7 13029596 13029675 1 1 1 16 0 65 12 | chr7 13029996 13030082 1 1 1 25 0 75 13 | chr7 13030207 13030288 1 1 1 24 0 72 14 | chr7 13030376 13030454 1 1 1 17 0 72 15 | chr7 13030593 13030688 1 1 1 21 0 72 16 | chr7 13032203 13032288 2 2 1 22 0 62 17 | chr7 13032351 13032434 2 2 1 18 0 62 18 | chr7 13032566 13032641 2 2 1 17 0 73 19 | chr7 13032822 13033828 2 2 1 11 0 70 20 | chr7 13034043 13034634 2 2 1 8 0 49 21 | chr7 130538253 130539010 2 2 1 1 0 62 22 | chr7 130542811 130545894 2 2 1 1 0 52 23 | chr7 130545973 130546991 2 2 1 1 0 21 24 | chr7 130877895 130882329 1 1 1 2 0 57 25 | chr7 130882387 130885402 1 1 1 1 0 25 26 | chr7 130892279 130897324 1 1 1 2 0 46 27 | chr7 130897451 130900516 1 1 1 3 0 52 28 | chr7 130908426 130909587 1 1 1 1 0 38 29 | chr7 130909629 130910831 1 1 1 1 0 41 30 | -------------------------------------------------------------------------------- /outrigger/tests/data/treutlein2014/unprocessed/sj_out_tab/SRR1034037_1.polyATrim.adapterTrim.rmRep.bamSJ.out.tab: -------------------------------------------------------------------------------- 1 | chr7 13025062 13025303 1 1 1 1 0 27 2 | chr7 13025417 13025643 1 1 1 2 0 49 3 | chr7 13025777 13027616 1 1 1 5 0 57 4 | chr7 13027753 13027832 1 1 1 2 0 53 5 | chr7 13027950 13028020 1 1 1 1 0 13 6 | chr7 13028555 13028663 1 1 1 1 0 45 7 | chr7 13028779 13028880 1 1 1 2 0 63 8 | chr7 13028988 13029087 1 1 1 1 0 37 9 | chr7 13029125 13029206 1 1 1 1 0 37 10 | chr7 13029596 13029675 1 1 1 2 0 65 11 | chr7 13029996 13030082 1 1 1 2 0 64 12 | chr7 13030593 13030688 1 1 1 2 0 72 13 | chr7 130167809 130169738 2 2 1 1 0 11 14 | chr7 130509259 130510810 2 2 1 5 0 62 15 | chr7 130510915 130513761 2 2 1 4 0 50 16 | chr7 130513825 130516104 2 2 1 3 0 51 17 | chr7 130516169 130519876 2 2 1 3 0 53 18 | chr7 130936744 130961512 1 1 1 3 0 59 19 | chr7 130961613 130961972 1 1 1 3 0 70 20 | chr7 130962178 130979300 1 1 1 1 0 45 21 | chr7 130979496 130979951 1 1 1 7 0 33 22 | chr7 130979985 130981656 1 1 1 6 0 33 23 | chr7 130981772 130982236 1 1 1 4 0 58 24 | chr7 130982295 130983659 1 1 1 2 0 58 25 | chr7 130983756 130984962 1 1 1 6 0 65 26 | -------------------------------------------------------------------------------- /outrigger/tests/data/treutlein2014/unprocessed/sj_out_tab/SRR1034038_1.polyATrim.adapterTrim.rmRep.bamSJ.out.tab: -------------------------------------------------------------------------------- 1 | chr7 13032566 13032641 2 2 1 2 0 57 2 | chr7 130507700 130509006 2 2 1 7 0 45 3 | chr7 130509259 130510810 2 2 1 28 0 74 4 | chr7 130510915 130513761 2 2 1 27 0 63 5 | chr7 130513825 130516104 2 2 1 18 0 63 6 | chr7 130516169 130519355 2 2 1 15 0 64 7 | -------------------------------------------------------------------------------- /outrigger/tests/data/treutlein2014/unprocessed/sj_out_tab/SRR1034039_1.polyATrim.adapterTrim.rmRep.bamSJ.out.tab: -------------------------------------------------------------------------------- 1 | chr7 130961613 130961972 1 1 1 2 0 69 2 | chr7 130962178 130979300 1 1 1 1 0 56 3 | -------------------------------------------------------------------------------- /outrigger/tests/data/treutlein2014/unprocessed/sj_out_tab/SRR1034040_1.polyATrim.adapterTrim.rmRep.bamSJ.out.tab: -------------------------------------------------------------------------------- 1 | chr7 13029996 13030082 1 1 1 1 0 67 2 | chr7 13032203 13032288 2 2 1 5 0 62 3 | chr7 13032351 13032434 2 2 1 6 0 62 4 | chr7 13032566 13032641 2 2 1 4 0 43 5 | chr7 13032822 13033828 2 2 1 3 0 69 6 | chr7 13034043 13034634 2 2 1 3 0 64 7 | -------------------------------------------------------------------------------- /outrigger/tests/data/treutlein2014/unprocessed/sj_out_tab/SRR1034042_1.polyATrim.adapterTrim.rmRep.bamSJ.out.tab: -------------------------------------------------------------------------------- 1 | chr7 13025777 13027616 1 1 1 10 0 53 2 | chr7 13027753 13027832 1 1 1 9 0 57 3 | chr7 13027950 13028020 1 1 1 10 0 74 4 | chr7 13028136 13028407 1 1 1 16 0 66 5 | chr7 13028555 13028663 1 1 1 7 0 50 6 | chr7 13028779 13028880 1 1 1 13 0 72 7 | chr7 13028988 13029087 1 1 1 7 0 37 8 | chr7 13029125 13029206 1 1 1 8 0 38 9 | chr7 13029253 13029342 1 1 1 10 0 46 10 | chr7 13029596 13029675 1 1 1 12 0 75 11 | chr7 13029996 13030082 1 1 1 12 0 72 12 | chr7 13030207 13030288 1 1 1 18 0 73 13 | chr7 13030376 13030454 1 1 1 15 0 64 14 | chr7 13030593 13030688 1 1 1 27 0 72 15 | chr7 13032203 13032288 2 2 1 29 0 64 16 | chr7 13032351 13032434 2 2 1 30 0 62 17 | chr7 13032566 13032641 2 2 1 18 0 73 18 | chr7 13032822 13033828 2 2 1 12 0 59 19 | chr7 13034043 13034634 2 2 1 10 0 75 20 | -------------------------------------------------------------------------------- /outrigger/tests/data/treutlein2014/unprocessed/sj_out_tab/SRR1034043_1.polyATrim.adapterTrim.rmRep.bamSJ.out.tab: -------------------------------------------------------------------------------- 1 | chr7 130877895 130882329 1 1 1 15 0 58 2 | chr7 130882387 130885402 1 1 1 13 0 46 3 | chr7 130885449 130892180 1 1 1 9 0 46 4 | -------------------------------------------------------------------------------- /outrigger/tests/data/treutlein2014/unprocessed/sj_out_tab/SRR1034044_1.polyATrim.adapterTrim.rmRep.bamSJ.out.tab: -------------------------------------------------------------------------------- 1 | chr7 13032203 13032288 2 2 1 1 0 50 2 | chr7 13032351 13032434 2 2 1 2 0 62 3 | chr7 13034043 13034634 2 2 1 2 0 52 4 | chr7 130532693 130533576 2 2 1 11 0 54 5 | chr7 130533667 130533769 2 2 1 13 0 58 6 | chr7 130533862 130535523 2 2 1 11 0 50 7 | chr7 130535573 130536982 2 2 1 8 0 49 8 | chr7 130537078 130538161 2 2 1 7 0 58 9 | chr7 130538253 130539010 2 2 1 7 0 74 10 | chr7 130539111 130539813 2 2 1 5 0 74 11 | chr7 130539966 130542679 2 2 1 2 0 47 12 | -------------------------------------------------------------------------------- /outrigger/tests/data/treutlein2014/unprocessed/sj_out_tab/SRR1034045_1.polyATrim.adapterTrim.rmRep.bamSJ.out.tab: -------------------------------------------------------------------------------- 1 | chr7 130182763 130185228 2 2 1 1 0 13 2 | chr7 130185381 130196177 2 2 1 1 0 4 3 | chr7 130516169 130519355 2 2 1 1 0 64 4 | -------------------------------------------------------------------------------- /outrigger/tests/data/treutlein2014/unprocessed/sj_out_tab/SRR1034046_1.polyATrim.adapterTrim.rmRep.bamSJ.out.tab: -------------------------------------------------------------------------------- 1 | chr7 130509259 130510810 2 2 1 1 0 39 2 | chr7 130510915 130513761 2 2 1 1 0 48 3 | -------------------------------------------------------------------------------- /outrigger/tests/data/treutlein2014/unprocessed/sj_out_tab/SRR1034047_1.polyATrim.adapterTrim.rmRep.bamSJ.out.tab: -------------------------------------------------------------------------------- 1 | chr7 13032203 13032288 2 2 1 6 0 63 2 | chr7 13032351 13032434 2 2 1 4 0 62 3 | chr7 13032566 13032641 2 2 1 8 0 72 4 | chr7 13032822 13033828 2 2 1 7 0 70 5 | chr7 13034043 13034634 2 2 1 6 0 61 6 | chr7 130394737 130418447 2 2 1 8 0 70 7 | chr7 130418569 130464130 2 2 1 6 0 53 8 | chr7 130537078 130538161 2 2 1 1 0 9 9 | chr7 130538253 130539010 2 2 1 1 0 51 10 | chr7 130539966 130542679 2 2 1 1 0 9 11 | chr7 130542811 130545894 2 2 1 1 0 11 12 | -------------------------------------------------------------------------------- /outrigger/tests/data/treutlein2014/unprocessed/sj_out_tab/SRR1034048_1.polyATrim.adapterTrim.rmRep.bamSJ.out.tab: -------------------------------------------------------------------------------- 1 | chr7 130164124 130167702 2 2 1 15 1 72 2 | chr7 130164216 130167702 2 2 1 0 1 8 3 | chr7 130167809 130169738 2 2 1 13 1 60 4 | chr7 130169877 130171611 2 2 1 11 0 70 5 | chr7 130171683 130172816 2 2 1 7 0 66 6 | chr7 130172940 130177674 2 2 1 1 0 46 7 | chr7 130196375 130199757 2 2 1 1 0 75 8 | chr7 130509259 130510810 2 2 1 1 0 71 9 | -------------------------------------------------------------------------------- /outrigger/tests/data/treutlein2014/unprocessed/sj_out_tab/SRR1034049_1.polyATrim.adapterTrim.rmRep.bamSJ.out.tab: -------------------------------------------------------------------------------- 1 | chr7 13029996 13030082 1 1 1 2 0 68 2 | chr7 13030207 13030288 1 1 1 5 0 72 3 | chr7 13030376 13030454 1 1 1 6 0 75 4 | chr7 13030593 13030688 1 1 1 11 0 75 5 | chr7 13032203 13032288 2 2 1 3 0 36 6 | chr7 13032351 13032434 2 2 1 6 0 62 7 | chr7 13032566 13032641 2 2 1 7 0 74 8 | chr7 13032822 13033828 2 2 1 4 0 46 9 | chr7 13034043 13034634 2 2 1 2 0 66 10 | chr7 130177866 130180364 2 2 1 1 0 4 11 | chr7 130180476 130182640 2 2 1 1 0 36 12 | chr7 130185381 130196177 2 2 1 1 0 28 13 | chr7 130509259 130510810 2 2 1 1 0 41 14 | chr7 130510915 130513761 2 2 1 1 0 6 15 | chr7 130513825 130516104 2 2 1 1 0 64 16 | chr7 130516169 130519355 2 2 1 1 0 23 17 | -------------------------------------------------------------------------------- /outrigger/tests/data/treutlein2014/unprocessed/sj_out_tab/SRR1034050_1.polyATrim.adapterTrim.rmRep.bamSJ.out.tab: -------------------------------------------------------------------------------- 1 | chr7 130167809 130169738 2 2 1 1 0 11 2 | chr7 130172940 130177674 2 2 1 1 0 48 3 | chr7 130219122 130228622 2 2 1 1 0 33 4 | chr7 130513825 130516104 2 2 1 1 0 3 5 | chr7 130516169 130519355 2 2 1 1 0 64 6 | -------------------------------------------------------------------------------- /outrigger/tests/data/treutlein2014/unprocessed/sj_out_tab/SRR1034051_1.polyATrim.adapterTrim.rmRep.bamSJ.out.tab: -------------------------------------------------------------------------------- 1 | chr7 13032203 13032288 2 2 1 5 0 62 2 | chr7 13032351 13032434 2 2 1 9 0 53 3 | chr7 13032566 13032641 2 2 1 9 0 65 4 | chr7 13032822 13033828 2 2 1 11 0 71 5 | chr7 13034043 13034634 2 2 1 5 0 53 6 | chr7 130509259 130510810 2 2 1 14 0 74 7 | chr7 130510915 130513761 2 2 1 13 0 63 8 | chr7 130513825 130516104 2 2 1 11 0 64 9 | chr7 130516169 130519355 2 2 1 8 0 64 10 | chr7 130897451 130900516 1 1 1 5 0 74 11 | chr7 130900661 130902176 1 1 1 5 0 69 12 | chr7 130902246 130904869 1 1 1 4 0 65 13 | chr7 130904935 130905390 1 1 1 5 0 20 14 | chr7 130905455 130908335 1 1 1 4 0 64 15 | chr7 130908426 130910831 1 1 1 3 0 66 16 | -------------------------------------------------------------------------------- /outrigger/tests/data/treutlein2014/unprocessed/sj_out_tab/SRR1034052_1.polyATrim.adapterTrim.rmRep.bamSJ.out.tab: -------------------------------------------------------------------------------- 1 | chr7 13030207 13030288 1 1 1 3 0 13 2 | chr7 13030376 13030454 1 1 1 5 0 75 3 | chr7 13030593 13030688 1 1 1 11 0 72 4 | chr7 130164216 130167702 2 2 1 32 0 75 5 | chr7 130167809 130169738 2 2 1 30 0 73 6 | chr7 130169877 130171611 2 2 1 25 0 71 7 | chr7 130171683 130172816 2 2 1 18 0 70 8 | chr7 130172940 130177674 2 2 1 30 0 71 9 | chr7 130177866 130180364 2 2 1 17 0 71 10 | chr7 130180476 130182640 2 2 1 24 0 75 11 | chr7 130182763 130185228 2 2 1 28 0 72 12 | chr7 130185381 130196171 0 0 1 27 0 75 13 | chr7 130196375 130199757 2 2 1 22 0 75 14 | chr7 130199906 130200982 2 2 1 26 0 75 15 | chr7 130201174 130218997 2 2 1 19 0 74 16 | chr7 130219122 130228622 2 2 1 14 0 75 17 | chr7 130228793 130241199 2 2 1 25 0 73 18 | chr7 130241278 130242377 2 2 1 21 0 72 19 | chr7 130242645 130261748 2 2 1 21 0 72 20 | chr7 130262067 130264301 2 2 0 7 0 24 21 | chr7 130262067 130265793 2 2 1 0 2 9 22 | chr7 130509259 130510810 2 2 1 1 0 39 23 | chr7 130510915 130513761 2 2 1 2 0 24 24 | chr7 130513825 130516104 2 2 1 1 0 63 25 | chr7 130516169 130519355 2 2 1 1 0 64 26 | chr7 130532693 130533576 2 2 1 17 0 60 27 | chr7 130533667 130533769 2 2 1 21 0 71 28 | chr7 130533862 130535523 2 2 1 26 0 50 29 | chr7 130535573 130536982 2 2 1 28 0 49 30 | chr7 130537078 130538161 2 2 1 21 0 74 31 | chr7 130538253 130539010 2 2 1 14 0 70 32 | chr7 130982295 130983659 1 1 1 3 0 45 33 | chr7 130983756 130984962 1 1 1 4 0 54 34 | -------------------------------------------------------------------------------- /outrigger/tests/data/treutlein2014/unprocessed/sj_out_tab/SRR1034053_1.polyATrim.adapterTrim.rmRep.bamSJ.out.tab: -------------------------------------------------------------------------------- 1 | chr7 13032203 13032288 2 2 1 6 0 63 2 | chr7 13032351 13032434 2 2 1 4 0 62 3 | chr7 13032566 13032641 2 2 1 2 0 62 4 | chr7 13032822 13033828 2 2 1 9 0 74 5 | chr7 13034043 13034634 2 2 1 8 0 74 6 | -------------------------------------------------------------------------------- /outrigger/tests/index/__init__.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/YeoLab/outrigger/9da86d2d8d137b309a53cae8851ba867cf757201/outrigger/tests/index/__init__.py -------------------------------------------------------------------------------- /outrigger/tests/io/__init__.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/YeoLab/outrigger/9da86d2d8d137b309a53cae8851ba867cf757201/outrigger/tests/io/__init__.py -------------------------------------------------------------------------------- /outrigger/tests/io/test_gtf.py: -------------------------------------------------------------------------------- 1 | import gffutils 2 | import pytest 3 | 4 | 5 | def test_create_db(gtf_filename, db, snap25_exon_id): 6 | from outrigger.io import gtf 7 | 8 | true = db 9 | test = gtf.create_db(gtf_filename, 'test.gtf.db') 10 | 11 | # Check that all the true db features are in the test database 12 | for featuretype in true.featuretypes(): 13 | for feature in true.features_of_type(featuretype=featuretype): 14 | try: 15 | test[feature.id] 16 | except gffutils.FeatureNotFoundError: 17 | pytest.fail('Feature in true database not found in test ' 18 | 'database') 19 | 20 | # Check that all the test db features are in the true database 21 | for featuretype in test.featuretypes(): 22 | for feature in test.features_of_type(featuretype=featuretype): 23 | try: 24 | true[feature.id] 25 | except gffutils.FeatureNotFoundError: 26 | pytest.fail('Feature in test database not found in true ' 27 | 'database') 28 | 29 | # SNAP25 should be in both the true and test databases 30 | assert true[snap25_exon_id] is not None 31 | assert test[snap25_exon_id] is not None 32 | -------------------------------------------------------------------------------- /outrigger/tests/psi/__init__.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/YeoLab/outrigger/9da86d2d8d137b309a53cae8851ba867cf757201/outrigger/tests/psi/__init__.py -------------------------------------------------------------------------------- /outrigger/tests/test.bed: -------------------------------------------------------------------------------- 1 | chr1 400 425 exon4_positive . + 2 | chr1 400 425 exon4_negative . - 3 | chr1 100 125 exon1alt_positive . + 4 | chr1 100 125 exon1alt_negative . - 5 | chr1 225 275 exon2a5ss_positive . + 6 | chr1 225 275 exon2a5ss_negative . - 7 | chr1 150 175 exon1_positive . + 8 | chr1 150 175 exon1_negative . - 9 | chr1 300 350 exon3_positive . + 10 | chr1 300 350 exon3_negative . - 11 | chr1 225 250 exon2_positive . + 12 | chr1 225 250 exon2_negative . - 13 | chr1 200 250 exon2a3ss_positive . + 14 | chr1 200 250 exon2a3ss_negative . - 15 | chr1 475 500 exon4alt_positive . + 16 | chr1 475 500 exon4alt_negative . - 17 | -------------------------------------------------------------------------------- /outrigger/tests/test.chromsizes: -------------------------------------------------------------------------------- 1 | chr1 600 2 | -------------------------------------------------------------------------------- /outrigger/tests/test.fasta: -------------------------------------------------------------------------------- 1 | >chr1 2 | CAGATTTTGCGAAGTACCACGAGTAGGAAGCCATCCATGACTTACTTGGTACAATCTGGC 3 | GTGAACTTGAGCACATTGAATAATTACACAATAGCCATAGATTGGCTCAGTGTAAGTGCT 4 | AGTGGCTTGTATAGGCACAAACGGCTTGCTGAGTAAATGCTGTCTGTCCCGAAGAGAACC 5 | CATAACGTGGAGGGAATAAATTTGTTGGGGAAGTAGTATCTCATTCATGGAGCCAAAGAC 6 | AGACGGTGTTGTCGATAGTCAAAGCTCTCAGTACTGTCACTAGGCTGCTTCTTTCGCCTA 7 | TGCGGATGTTGCCTGGTCGAGTGGAGCGTATTTCCATACCTATTCAATGTAACAACGTCA 8 | TCGCTCCATAGGGCGCCTAAGGCGTACCATAGTAATTGAACCGGGGACGGCGTGTACAGG 9 | TAGAGAATGGCACCCTACAGTTTGTGACAGTCGGAGGCCGGGCAGTGATTGGTGGGAATA 10 | TAGCCCGGATCCGCTCGTAATCTCTAAATTTATTGACCCAGTTACGTTAGATTGCTGTTA 11 | CACGAGTCAGTACATATCTGATGCGACCGTGCTCTAGGCACGGCAGGCAACGTCTTGCAC 12 | -------------------------------------------------------------------------------- /outrigger/tests/test.fasta.fai: -------------------------------------------------------------------------------- 1 | chr1 600 6 60 61 2 | -------------------------------------------------------------------------------- /outrigger/tests/validate/__init__.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/YeoLab/outrigger/9da86d2d8d137b309a53cae8851ba867cf757201/outrigger/tests/validate/__init__.py -------------------------------------------------------------------------------- /outrigger/util.py: -------------------------------------------------------------------------------- 1 | import datetime 2 | import sys 3 | 4 | 5 | def timestamp(): 6 | return str(datetime.datetime.now().strftime('%Y-%m-%d %H:%M:%S')) 7 | 8 | 9 | def done(n_tabs=2): 10 | """Write timestamp plus 'Done.' to stdout 11 | 12 | Parameters 13 | ---------- 14 | n_tabs : int 15 | Number of tabs to include. Default is 2 16 | """ 17 | sys.stdout.write('{}{}Done.\n'.format(timestamp(), '\t' * n_tabs)) 18 | 19 | 20 | def progress(message): 21 | """Write a timestamped progress message to standard output""" 22 | sys.stdout.write('{}\t{}\n'.format(timestamp(), message)) 23 | 24 | 25 | def extract_alternative_constitutive(psi): 26 | """Separate psi matrix to events that are alternative vs constitutive 27 | 28 | Parameters 29 | ---------- 30 | psi : pandas.DataFrame 31 | This is a (samples, features) shaped dataframe of the percent 32 | spliced-in values 33 | 34 | Returns 35 | ------- 36 | alternative, constitutively0, constitutively1 : pandas.DataFrame 37 | Slices of the input dataframe that are alternative or constitutive 38 | """ 39 | 40 | notnull = psi.notnull() 41 | 42 | constitutively0 = (psi == 0)[notnull].all() 43 | constitutively1 = (psi == 1)[notnull].all() 44 | alternative = psi.columns[(~constitutively0) & (~constitutively1)] 45 | 46 | constitutively0 = constitutively0[constitutively0].index 47 | constitutively1 = constitutively1[constitutively1].index 48 | 49 | return psi[alternative], psi[constitutively0], psi[constitutively1] 50 | -------------------------------------------------------------------------------- /outrigger/validate/__init__.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/YeoLab/outrigger/9da86d2d8d137b309a53cae8851ba867cf757201/outrigger/validate/__init__.py -------------------------------------------------------------------------------- /requirements.txt: -------------------------------------------------------------------------------- 1 | pytest>=3.0.0 2 | pandas>=0.17.0 3 | coverage 4 | gffutils>=0.8.7.1 5 | pybedtools 6 | biopython 7 | joblib 8 | pysam 9 | graphlite 10 | pytest-cov 11 | -------------------------------------------------------------------------------- /setup.cfg: -------------------------------------------------------------------------------- 1 | [wheel] 2 | universal = 1 3 | -------------------------------------------------------------------------------- /testing/environment_no_python.yml: -------------------------------------------------------------------------------- 1 | name: outrigger-env 2 | channels: 3 | - conda-forge 4 | - r 5 | - bioconda 6 | dependencies: 7 | - pytest 8 | - pandas>=0.17.0 9 | - coverage 10 | - gffutils 11 | - pybedtools 12 | - biopython 13 | - bedtools 14 | - joblib 15 | - pysam 16 | - sphinx>=1.3.6 17 | - sphinx_rtd_theme 18 | - pip: 19 | - graphlite 20 | - recommonmark==0.4.0 21 | - nbsphinx 22 | --------------------------------------------------------------------------------