Make Reference

To build a genome reference index, StarScope included a subcommand mkref to help user achieve this via nextflow run.

starscope mkref --conda \
--conda_env /path/to/env \
--genomeFasta genome.fa \
--genomeGTF genes.gtf

The output index directory will be like:

results/STAR_reference/
├── 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

0 directories, 16 files

We also included a helper script to perform a 10X like filtration step on reference files downloaded from Ensembl, user could invoke with:

starscope/process_reference.sh --fasta origin_genome.fa.gz --gtf origin.gtf.gz

The output files are genome.fa and genes.gtf in the working directory.