├── LICENSE ├── Makefile ├── README.md ├── Rscripts ├── extract_observed_junctions.R ├── filter_fastq.R ├── generate_tx2gene.R ├── get_nbr_reads.R ├── get_nbr_reads_NA12878public.R ├── get_polyA_tail_lengths.R ├── get_reads_aligning_to_genome_but_not_txome.R ├── gff2gtf.R ├── list_packages.R ├── merge_promoter_bed_files.R ├── plot_abundances.R ├── plot_abundances_template.Rmd ├── plot_compare_flair_annotation.R ├── plot_distance_primary_supplementary_alignments.R ├── plot_eq_class_counts.R ├── plot_qc.R ├── summarize_abundances.R ├── summarize_abundances_illumina.R └── summarize_star_sjdbs.R ├── datasets_to_include.mk ├── manuscript_results_figures └── Rscripts │ ├── plot_alignment.R │ ├── plot_compare_gffcompare_sqanti.R │ ├── plot_consistency_between_replicates.R │ ├── plot_flair_round2_summary.R │ ├── plot_flair_summary.R │ ├── plot_gc_content_genomenotxome.R │ ├── plot_illumina_nanopore_lengths_all_datasets.R │ ├── plot_nbr_assigned_reads.R │ ├── plot_nbr_assigned_reads_biotype.R │ ├── plot_nbr_detected_features.R │ ├── plot_nbr_junctions_per_read_illumina.R │ ├── plot_nbr_reads.R │ ├── plot_nbr_tx_in_eqclass.R │ ├── plot_observed_junctions.R │ ├── plot_palindromes.R │ ├── plot_polya_tail_estimates.R │ ├── plot_primary_supplementary.R │ ├── plot_rseqc.R │ ├── plot_salmon_variants_all_datasets.R │ ├── plot_sqanti_round2_summary.R │ ├── plot_sqanti_summary.R │ ├── plot_txcov_sirv.R │ ├── plot_txcov_subsampling.R │ ├── plot_txlength_vs_basecoverage.R │ └── remap_sample_names.R └── reference └── chromhmm_promoters └── hg38_promoters.bed /LICENSE: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/csoneson/NativeRNAseqComplexTranscriptome/HEAD/LICENSE -------------------------------------------------------------------------------- /Makefile: -------------------------------------------------------------------------------- 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