I have genome reference, annotation files and hisat2-index from Hisat2 website
GENCODE gene annotation: ftp://ftp.ebi.ac.uk/pub/databases/gencode/Gencode_human/release_27/gencode.v27.annotation.gtf.gz
hisat2 index : genome_snp_tran (GRch38) from [https://ccb.jhu.edu/software/hisat2/index.shtml]
I see that genome.fa and gencode gtf file has chromosome names with
chr started. But the hisat-2 index file doesn't have
chr in it.
Should I remove
chr from fasta and gtf files? Or should I build own hisat2-index?