A .gtf file for HG38 for HISAT2 indexing I am trying to build a HISAT2 index using Pertea et al. procedure (https://www.ncbi.nlm.nih.gov/pubmed/27560171) using their extract_splice_sites.py and 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 &gt; 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.
I had the same problem and I was able to solve it with that
https://github.com/NBISweden/GAAS/blob/master/annotation/knowledge/gff_to_gtf.md