Hello, I found this code in Biostar handbook (RNA-Seq by Example) in section about genome indexing.
# The reference genome. IDX=refs/genome.fa # Build the genome index. hisat2-build $IDX $IDX # Index the reference genome with samtools. samtools faidx $IDX
I was wondering about samtools indexing step. I've never seen anyone using it before. Isn't hisat2-build not enough to properly index genome?