/coalispr/docs/_source/tutorials/H99/shared/
├── 0_0-SRAaccess.sh
├── 0_1-SRAaccess.sh
├── 0_2-gzip-fastq.sh
├── 1_0-flexbar-trim.sh
├── 2_0-collapse.sh
├── 3_0-createSTARindex.sh
├── 3_1-run-star-collapsed-14mer-strict.sh
├── 3_1_1-run-make-SJDB.sh
├── 3_2-run-make-bedgraphs.sh
├── 3_2_0-run-sortBAM-star-Bedgraph.sh
├── 4_1-run-star-uncollapsed-14mer-strict.sh
├── 4_2-run-make-bedgraphs-uncollapsed.sh
├── 5_1-QC-reports.sh
├── 5_1_0-run-RSeQC-bam_stat-FASTQC.sh
├── check
│ ├── 2_SraRunTable.txt
│ ├── 3_h99.txt
│ ├── SRR_Acc_List.txt
│ ├── SraRunTable.txt
│ ├── h99-chr-lengths.txt
| ├── h99-siRNAsegments.gtf
│ ├── mito.gtf
│ └── ncRNA-pseu.gtf
└── source
├── NAT_G418_HYG.gbk
├── NAT_G418_HYG.fa
├── SpliceJunctionDataBase-sorted-uniq.txt
├── h99-experiment_table.tsv
├── h99-ncRNAxtra.gtf
├── h99-siRNAsegments.tsv
└── h99-xtra.gtf