Which GTF and Fasta version to use
| File | Content | Regions | Description |
|---|---|---|---|
| GTF | Comprehensive gene annotation | CHR | It contains the comprehensive gene annotation on the reference chromosomes only |
| Fasta | Genome sequence, primary assembly (GRCm39) | PRI | Nucleotide sequence of the GRCm39 primary genome assembly (chromosomes and scaffolds) The sequence region names are the same as in the GTF/GFF3 files |
Reference: https://github.com/alexdobin/STAR/issues/421#issue-324114662