├── BRIC-seq_Tutorial ├── BRIC-seq_test_run.sh ├── BRIC-seq_unstr_single-end_1_mapping.sh ├── BRIC-seq_unstr_single-end_2_RPKM_calc_Control.sh ├── BRIC-seq_unstr_single-end_2_RPKM_calc_Knockdown.sh ├── BRIC-seq_unstr_single-end_3_RNA_half-life_calc.sh ├── BridgeR_analysis_lncRNA.R ├── BridgeR_analysis_mRNA.R ├── BridgeR_prep.py ├── BridgeR_shinyapp.R ├── extract_gene_symbol_type_from_gtf.py └── sra_download_BRIC-seq.sh ├── LICENSE ├── PAR-CLIP_Tutorial_CstF64 ├── 2016-01-17_Base_substitution_frequency.xlsx ├── A_prep_gtf_for_PAR-CLIP.py ├── B_prep_longest_trx_id_list.py ├── C_prep_fasta_file_for_MEME.py ├── D_prep_fasta_file_for_MEME_rep_version.py ├── E_mismatch_call_from_bam.py ├── E_mismatch_call_from_bam_for_TopHat.py ├── F_split_into_each_section.py ├── G_add_intron_infor.py ├── H_annotate_peaks.py ├── I_prep_mRNA_lncRNA_symbol_refid_list.py ├── PAR-CLIP_CstF-64.sh ├── PARalyzer2BEDandFASTA.py ├── PARalyzer_ini_file_generator.py ├── PARalyzer_v1_5.ini ├── PARalyzer_v1_5.sh ├── bed12to3UTRbed ├── bed12to3UTRbed.pl ├── bed2fasta ├── compare_annotation_3UTR_with_peaks.sh ├── extract_gene_symbol_type_from_gtf.py ├── gtf2bed ├── gtf2bed.pl ├── logo1.png ├── logo2.png ├── meme.html ├── motif_discovery_using_MEME.sh ├── motif_discovery_using_MEME_rep_version.sh ├── peak_anno.sh ├── prep_MEME_background_data.sh ├── prep_anno_list_for_user.sh ├── prep_gtf_for_PAR-CLIP_analysis.sh ├── star-prep1-getDNAsequence.sh ├── star-prep2-generate_genomic_index_files_repBase_rRNA.sh └── variant_calling_for_PAR-CLIP_data_checking.sh ├── README.md ├── RNA-seq_Tutorial ├── RNA-seq_test_run.sh ├── RNA-seq_unstr_single-end_1_mapping.sh ├── RNA-seq_unstr_single-end_2_cuffdiff_calc.sh ├── RNA-seq_unstr_single-end_2_edgeR_calc.sh ├── annotate_gene_symbol_type.py ├── cuffdiff_result.py ├── edgeR_test.R ├── extract_gene_symbol_type_from_gtf.py └── split_into_each_gene_type.py ├── RNA-seq_for_alternative_splicing_Tutorial ├── DEXSeq_check.py ├── DEXSeq_test.R ├── DEXSeq_test.sh ├── MISO_annotation_prep.sh ├── MISO_comparison.sh ├── MISO_test.sh ├── RNA-seq_strand-specific_single-end_1_mapping_for_AS.sh ├── miso_settings.txt └── rMATS_test.sh ├── Ribo-seq_RiboTaper ├── 2016-03-15_Ribo-seq_data_list.xlsx ├── Final_ORF_results.pdf ├── ORFs_genes_found ├── Ribo-seq-RiboTaper-0-QC.sh ├── Ribo-seq-RiboTaper-0-create_annotation.sh ├── Ribo-seq-RiboTaper-0-sra_download.sh ├── Ribo-seq-RiboTaper-1-triming_adapter.sh ├── Ribo-seq-RiboTaper-2-mapping.sh ├── Ribo-seq-RiboTaper-3-create_metaplots.sh ├── Ribo-seq-RiboTaper-3-define_ORF_STEP1.sh ├── Ribo-seq-RiboTaper-3-define_ORF_STEP2-1.sh ├── Ribo-seq-RiboTaper-3-define_ORF_STEP2-2.sh ├── Ribo-seq-RiboTaper-3-define_ORF_STEP2-3.sh ├── Ribo-seq-RiboTaper-3-define_ORF_STEP3.sh ├── Ribo-seq-RiboTaper-3-define_ORF_STEP4.sh ├── RiboTaper_v1.3_README ├── Ribotaper_step1.sh ├── Ribotaper_step2-1.sh ├── Ribotaper_step2-2.sh ├── Ribotaper_step2-3.sh ├── Ribotaper_step3.sh ├── Ribotaper_step4.sh ├── quality_check_plots.pdf ├── scripts │ ├── CCDS_orf_finder.R │ ├── CCDS_orf_finder_single.R │ ├── NONCCDS_orf_finder.R │ ├── ORF_final_results.R │ ├── P_sites_RNA_sites_calc.bash │ ├── Ribotaper.sh │ ├── Ribotaper_ORF_find.sh │ ├── Ribotaper_step1.sh │ ├── Ribotaper_step2-1.sh │ ├── Ribotaper_step2-2.sh │ ├── Ribotaper_step2-3.sh │ ├── Ribotaper_step3.sh │ ├── Ribotaper_step4.sh │ ├── analyze_multi_clust.bash │ ├── annotate_exons.R │ ├── bowrrna_star.q │ ├── create_annotations_files.bash │ ├── create_metaplots.bash │ ├── create_protein_db.R │ ├── create_tracks.bash │ ├── fastCoverage.py │ ├── functions.R │ ├── genes_coor.R │ ├── gtf_to_start_stop_tr.R │ ├── include_multi_nomerge.R │ ├── metag.R │ ├── quality_check.R │ ├── tracks_analysis.R │ ├── tracks_analysis_single.R │ └── write_startstops.R ├── star-prep1-getDNAsequence.sh ├── star-prep2-generate_genomic_index_files_hg19_Gencode_v19.sh └── star-prep2-generate_genomic_index_files_rRNA.sh └── Strand-specific_RNA-seq_Tutorial ├── 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