11.1. STAR Genomic Indexes¶
The genome.fa and genes.gtf files should be copied to the genome directory.
localhost:~> mkdir genome
localhost:~> cd genome
localhost:~> mkdir STAR
localhost:~> cd STAR
localhost:~> cwl-runner https://github.com/ncbi/cwl-ngs-workflows-cbb/blob/master/tools/star/star-index.cwl --runThreadN 16 --genomeDir . --genomeFastaFiles ../genome.fa --sjdbGTFfile ../genes.gtf
localhost:~> cd ..
localhost:~> tree
.
├── genes.gtf
├── genome.fa
└── STAR
├── chrLength.txt
├── chrNameLength.txt
├── chrName.txt
├── chrStart.txt
├── exonGeTrInfo.tab
├── exonInfo.tab
├── geneInfo.tab
├── Genome
├── genomeParameters.txt
├── Log.out
├── SA
├── SAindex
├── sjdbInfo.txt
├── sjdbList.fromGTF.out.tab
├── sjdbList.out.tab
└── transcriptInfo.tab
1 directory, 18 files
Here all files inside the directory STAR are created by the workflow.