I am trying to build a HISAT2 index using Pertea et al. procedure (https://www.ncbi.nlm.nih.gov/pubmed/27560171) using their
extract_exons.py pieces of code. For that, I need a
.gtf file of Human Genome HG38. I have obtained this file using recommendations described here http://www.metagenomics.wiki/tools/fastq/ncbi-ftp-genome-download
The file I have downloaded is
GCF_000001405.39_GRCh38.p13_genomic.gff (1,1 Gb) and when I use on it this command
python3 extract_splice_sites.py GCF_000001405.39_GRCh38.p13_genomic.gff > test.ss my
test.ss file is 0 Kb! I wonder if there's another
.gff file that I must use and where I can get it? This is my first time working with the human genome so I am not sure if I am doing the procedure the right way.