text: user6948: 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 > 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.
  
  user6694: 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
  
original_text: 6948: <p>I am trying to build a HISAT2 index using Pertea et al. procedure (<a href="https://www.ncbi.nlm.nih.gov/pubmed/27560171" rel="nofollow noreferrer">https://www.ncbi.nlm.nih.gov/pubmed/27560171</a>) using their <code>extract_splice_sites.py</code> and <code>extract_exons.py</code> pieces of code. For that, I need a <code>.gtf</code> file of Human Genome HG38. I have obtained this file using recommendations described here <a href="http://www.metagenomics.wiki/tools/fastq/ncbi-ftp-genome-download" rel="nofollow noreferrer">http://www.metagenomics.wiki/tools/fastq/ncbi-ftp-genome-download</a></p>
  
  <p>The file I have downloaded is <code>GCF_000001405.39_GRCh38.p13_genomic.gff</code> (1,1 Gb) and when I use on it this command <code>python3 extract_splice_sites.py GCF_000001405.39_GRCh38.p13_genomic.gff &gt; test.ss</code> my <code>test.ss</code> file is 0 Kb! I wonder if there's another <code>.gff</code> 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.</p>
   6694: <p>I had the same problem and I was able to solve it with that
  <a href="https://github.com/NBISweden/GAAS/blob/master/annotation/knowledge/gff_to_gtf.md" rel="nofollow noreferrer">https://github.com/NBISweden/GAAS/blob/master/annotation/knowledge/gff_to_gtf.md</a></p>
  