Answers.Body: <p>You can download a GTF file from NCBI now. For hg38 (also known as GRCh38), just go to <a href="https://www.ncbi.nlm.nih.gov/assembly" rel="nofollow noreferrer">NCBI Assembly</a> and search for 'GRCh38'. Click on the first result to go to <a href="https://www.ncbi.nlm.nih.gov/assembly/GCF_000001405.39" rel="nofollow noreferrer">this page</a> and use the blue 'Download Assemblies' button to download data. Here, after you choose 'RefSeq' as your source of data, you will see a GTF file to download from the drop-down list, as shown in the screenshot below: 
  <a href="https://i.sstatic.net/iye4v.png" rel="nofollow noreferrer"><img src="https://i.sstatic.net/iye4v.png" alt="enter image description here"></a></p>
  
Answers.ContentLicense: CC BY-SA 4.0
Answers.CreationDate: 2020-04-20T00:50:16.947Z
Answers.LastActivityDate: 2020-04-20T00:50:16.947Z
Answers.UserDisplayName: vkkodali
Answers.Body: <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>
  
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Answers.CreationDate: 2020-04-21T20:58:25.367Z
Answers.LastActivityDate: 2020-04-21T20:58:25.367Z
Answers.UserDisplayName: Diango
Body: <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>
  
Comments.ContentLicense: CC BY-SA 4.0
Comments.CreationDate: 2020-04-20T16:00:59.560Z
Comments.Text: you might wanna try python2.7 https://www.biostars.org/p/293881/
Comments.UserDisplayName: StupidWolf
Tags: <python><gtf><human-genome>
Title: A .gtf file for HG38 for HISAT2 indexing
ThreadText: # A .gtf file for HG38 for HISAT2 indexing
  
  (Asked by: username_0 on 2020-04-19)
  
  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.
  
  **Tags:** python, gtf, human-genome
  
  > **Comments:**
  > **username_1**: you might wanna try python2.7 https://www.biostars.org/p/293881/  
  
  ---
  
  ## 2 answers
  
  ### Answer by username_2 on 2020-04-20. Score: 0 | Accepted answer
  
  You can download a GTF file from NCBI now. For hg38 (also known as GRCh38), just go to [NCBI Assembly](https://www.ncbi.nlm.nih.gov/assembly) and search for 'GRCh38'. Click on the first result to go to [this page](https://www.ncbi.nlm.nih.gov/assembly/GCF_000001405.39) and use the blue 'Download Assemblies' button to download data. Here, after you choose 'RefSeq' as your source of data, you will see a GTF file to download from the drop-down list, as shown in the screenshot below:
  [![enter image description here](https://i.sstatic.net/iye4v.png)](https://i.sstatic.net/iye4v.png)
  
  
  ---
  
  ### Answer by username_3 on 2020-04-21. Score: 1
  
  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>
  
  
  ---
  
  