Answers.Body: <p>You can use <code>gffread</code> to convert <code>gff</code> to <code>gtf2</code>, below is from <a href="http://ccb.jhu.edu/software/stringtie/gff.shtml" rel="noreferrer">the manual</a>:</p>
  
  <blockquote>
    <p>In order to see the GTF2 version of the same transcripts, the -T
    option should be added:</p>
  
  <pre><code>gffread -E annotation.gff -T -o- | more
  </code></pre>
    
    <p>The examples above also show that gffread can be used to convert a
    file between GTF2 and GFF3 file formats.</p>
  </blockquote>
  
Answers.ContentLicense: CC BY-SA 4.0
Answers.CreationDate: 2020-02-01T06:22:36.140Z
Answers.Text: Thk for your awnser
Answers.UserDisplayName: Diango
Answers.ContentLicense: CC BY-SA 4.0
Answers.CreationDate: 2019-12-29T09:46:01.213Z
Answers.LastActivityDate: 2019-12-29T09:46:01.213Z
Answers.UserDisplayName: haci
Answers.Body: <p>I would suggest to use <code>agat_convert_sp_gff2gtf.pl</code> from <a href="https://github.com/NBISweden/AGAT" rel="noreferrer">AGAT</a> because you loose information with <code>gffread</code>.<br>
  e.g here a gff example:</p>
  
  <pre><code>##gff-version 3
  scaffold625 maker   gene    337818  343277  .   +   .   ID=CLUHARG00000005458;Name=TUBB3_2
  scaffold625 maker   transcript  337818  343277  .   +   .   ID=CLUHART00000008717;Parent=CLUHARG00000005458
  scaffold625 maker   CDS 337915  337971  .   +   0   ID=CLUHART00000008717:cds;Parent=CLUHART00000008717
  scaffold625 maker   CDS 340733  340841  .   +   0   ID=CLUHART00000008717:cds;Parent=CLUHART00000008717
  scaffold625 maker   CDS 341518  341628  .   +   2   ID=CLUHART00000008717:cds;Parent=CLUHART00000008717
  scaffold625 maker   CDS 341964  343033  .   +   2   ID=CLUHART00000008717:cds;Parent=CLUHART00000008717
  scaffold625 maker   exon    337818  337971  .   +   0   ID=CLUHART00000008717:exon1;Parent=CLUHART00000008717
  scaffold625 maker   exon    340733  340841  .   +   0   ID=CLUHART00000008717:exon2;Parent=CLUHART00000008717
  scaffold625 maker   exon    341518  341628  .   +   2   ID=CLUHART00000008717:exon3;Parent=CLUHART00000008717
  scaffold625 maker   exon    341964  343277  .   +   2   ID=CLUHART00000008717:exon4;Parent=CLUHART00000008717
  scaffold625 maker   five_prime_UTR  337818  337914  .   +   .   ID=CLUHART00000008717:five_prime_utr;Parent=CLUHART00000008717
  scaffold625 maker   three_prime_UTR 343034  343277  .   +   .   ID=CLUHART00000008717:three_prime_utr;Parent=CLUHART00000008717
  </code></pre>
  
  <p>with gffread you get:</p>
  
  <pre><code>scaffold625 maker   transcript  337818  343277  .   +   .   transcript_id "CLUHART00000008717"; gene_id "CLUHARG00000005458";
  scaffold625 maker   exon    337818  337971  .   +   .   transcript_id "CLUHART00000008717"; gene_id "CLUHARG00000005458";
  scaffold625 maker   exon    340733  340841  .   +   .   transcript_id "CLUHART00000008717"; gene_id "CLUHARG00000005458";
  scaffold625 maker   exon    341518  341628  .   +   .   transcript_id "CLUHART00000008717"; gene_id "CLUHARG00000005458";
  scaffold625 maker   exon    341964  343277  .   +   .   transcript_id "CLUHART00000008717"; gene_id "CLUHARG00000005458";
  scaffold625 maker   CDS 337915  337971  .   +   0   transcript_id "CLUHART00000008717"; gene_id "CLUHARG00000005458";
  scaffold625 maker   CDS 340733  340841  .   +   0   transcript_id "CLUHART00000008717"; gene_id "CLUHARG00000005458";
  scaffold625 maker   CDS 341518  341628  .   +   2   transcript_id "CLUHART00000008717"; gene_id "CLUHARG00000005458";
  scaffold625 maker   CDS 341964  343033  .   +   2   transcript_id "CLUHART00000008717"; gene_id "CLUHARG00000005458";
  </code></pre>
  
  <p>while with AGAT you get</p>
  
  <pre><code>scaffold625 maker   gene    337818  343277  .   +   .   ID CLUHARG00000005458 ; Name TUBB3_2 ; gene_id CLUHARG00000005458
  scaffold625 maker   mRNA    337818  343277  .   +   .   ID CLUHART00000008717 ; Parent CLUHARG00000005458 ; gene_id CLUHARG00000005458 ; transcript_id CLUHART00000008717
  scaffold625 maker   exon    337818  337971  .   +   0   ID "CLUHART00000008717:exon1"  ; Parent CLUHART00000008717 ; gene_id CLUHARG00000005458 ; transcript_id CLUHART00000008717
  scaffold625 maker   exon    340733  340841  .   +   0   ID "CLUHART00000008717:exon2"  ; Parent CLUHART00000008717 ; gene_id CLUHARG00000005458 ; transcript_id CLUHART00000008717
  scaffold625 maker   exon    341518  341628  .   +   2   ID "CLUHART00000008717:exon3"  ; Parent CLUHART00000008717 ; gene_id CLUHARG00000005458 ; transcript_id CLUHART00000008717
  scaffold625 maker   exon    341964  343277  .   +   2   ID "CLUHART00000008717:exon4"  ; Parent CLUHART00000008717 ; gene_id CLUHARG00000005458 ; transcript_id CLUHART00000008717
  scaffold625 maker   CDS 337915  337971  .   +   0   ID "CLUHART00000008717:cds"  ; Parent CLUHART00000008717 ; gene_id CLUHARG00000005458 ; transcript_id CLUHART00000008717
  scaffold625 maker   CDS 340733  340841  .   +   0   ID "CLUHART00000008717:cds"  ; Parent CLUHART00000008717 ; gene_id CLUHARG00000005458 ; transcript_id CLUHART00000008717
  scaffold625 maker   CDS 341518  341628  .   +   2   ID "CLUHART00000008717:cds"  ; Parent CLUHART00000008717 ; gene_id CLUHARG00000005458 ; transcript_id CLUHART00000008717
  scaffold625 maker   CDS 341964  343033  .   +   2   ID "CLUHART00000008717:cds"  ; Parent CLUHART00000008717 ; gene_id CLUHARG00000005458 ; transcript_id CLUHART00000008717
  scaffold625 maker   five_prime_UTR  337818  337914  .   +   .   ID "CLUHART00000008717:five_prime_utr"  ; Parent CLUHART00000008717 ; gene_id CLUHARG00000005458 ; transcript_id CLUHART00000008717
  scaffold625 maker   three_prime_UTR 343034  343277  .   +   .   ID "CLUHART00000008717:three_prime_utr"  ; Parent CLUHART00000008717 ; gene_id CLUHARG00000005458 ; transcript_id CLUHART00000008717
  </code></pre>
  
  <p>So you can see as example that <code>Name=TUBB3_2</code> from the gene feature disappeared with <code>gffread</code>.</p>
  
Answers.ContentLicense: CC BY-SA 4.0
Answers.CreationDate: 2020-03-13T13:05:39.923Z
Answers.LastActivityDate: 2020-03-17T16:00:46.463Z
Answers.LastEditDate: 2020-03-17T16:00:46.463Z
Answers.UserDisplayName: juke34
Answers.Body: <p>You can try bioinfokit (<a href="https://github.com/reneshbedre/bioinfokit" rel="nofollow noreferrer">https://github.com/reneshbedre/bioinfokit</a>) in python.</p>
  <pre><code>from bioinfokit.analys import gff
  
  gff.gff_to_gtf(file=&quot;yourfile.gff3&quot;) 
  # The converted gtf file will be saved in the same working directory.
  <span class="math-container">```</span>
  </code></pre>
  
Answers.ContentLicense: CC BY-SA 4.0
Answers.CreationDate: 2021-12-21T18:02:55.693Z
Answers.LastActivityDate: 2021-12-23T20:11:09.687Z
Answers.LastEditDate: 2021-12-23T20:11:09.687Z
Answers.UserDisplayName: Liyong
Answers.Body: <p>Actually I started a mini-review about the tools to do such conversion.<br>
  You can find it here: 
  <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>
  
  <p>As I mentioned earlier they do not behave all the same way...</p>
  
Answers.ContentLicense: CC BY-SA 4.0
Answers.CreationDate: 2020-03-17T16:03:41.023Z
Answers.LastActivityDate: 2020-03-17T16:03:41.023Z
Answers.UserDisplayName: juke34
Body: <p>My annotation file is in .gff format. I would like to convert it to .gtf format or to know if there is a way to directly download the annotation file in .gtf format?</p>
  
  <p>I am working on sequences from the P Falicparum 3D7.</p>
  
Comments.ContentLicense: CC BY-SA 4.0
Comments.CreationDate: 2020-01-31T10:06:38.667Z
Comments.Text: I think the question was already extensively answered here:
  https://bioinformatics.stackexchange.com/questions/2068/how-to-convert-gff3-to-gtf2
Comments.UserDisplayName: aechchiki
Comments.ContentLicense: CC BY-SA 4.0
Comments.CreationDate: 2020-02-01T06:21:55.910Z
Comments.Text: Thank you for your awnser
Comments.UserDisplayName: Diango
Tags: <rna-seq><gtf><gff>
Title: How to convert gff to gtf?
ThreadText: # How to convert gff to gtf?
  
  (Asked by: username_0 on 2019-12-29)
  
  My annotation file is in .gff format. I would like to convert it to .gtf format or to know if there is a way to directly download the annotation file in .gtf format?
  
  I am working on sequences from the P Falicparum 3D7.
  
  **Tags:** rna-seq, gtf, gff
  
  > **Comments:**
  > **username_1**: I think the question was already extensively answered here: https://bioinformatics.stackexchange.com/questions/2068/how-to-convert-gff3-to-gtf2  
  > **username_0**: Thank you for your awnser  
  
  ---
  
  ## 4 answers
  
  ### Answer by username_3 on 2020-03-13. Score: 6
  
  I would suggest to use `agat_convert_sp_gff2gtf.pl` from [AGAT](https://github.com/NBISweden/AGAT) because you loose information with `gffread`.  
  e.g here a gff example:
  
  ```
  ##gff-version 3
  scaffold625 maker   gene    337818  343277  .   +   .   ID=CLUHARG00000005458;Name=TUBB3_2
  scaffold625 maker   transcript  337818  343277  .   +   .   ID=CLUHART00000008717;Parent=CLUHARG00000005458
  scaffold625 maker   CDS 337915  337971  .   +   0   ID=CLUHART00000008717:cds;Parent=CLUHART00000008717
  scaffold625 maker   CDS 340733  340841  .   +   0   ID=CLUHART00000008717:cds;Parent=CLUHART00000008717
  scaffold625 maker   CDS 341518  341628  .   +   2   ID=CLUHART00000008717:cds;Parent=CLUHART00000008717
  scaffold625 maker   CDS 341964  343033  .   +   2   ID=CLUHART00000008717:cds;Parent=CLUHART00000008717
  scaffold625 maker   exon    337818  337971  .   +   0   ID=CLUHART00000008717:exon1;Parent=CLUHART00000008717
  scaffold625 maker   exon    340733  340841  .   +   0   ID=CLUHART00000008717:exon2;Parent=CLUHART00000008717
  scaffold625 maker   exon    341518  341628  .   +   2   ID=CLUHART00000008717:exon3;Parent=CLUHART00000008717
  scaffold625 maker   exon    341964  343277  .   +   2   ID=CLUHART00000008717:exon4;Parent=CLUHART00000008717
  scaffold625 maker   five_prime_UTR  337818  337914  .   +   .   ID=CLUHART00000008717:five_prime_utr;Parent=CLUHART00000008717
  scaffold625 maker   three_prime_UTR 343034  343277  .   +   .   ID=CLUHART00000008717:three_prime_utr;Parent=CLUHART00000008717
  
  ```
  
  with gffread you get:
  
  ```
  scaffold625 maker   transcript  337818  343277  .   +   .   transcript_id "CLUHART00000008717"; gene_id "CLUHARG00000005458";
  scaffold625 maker   exon    337818  337971  .   +   .   transcript_id "CLUHART00000008717"; gene_id "CLUHARG00000005458";
  scaffold625 maker   exon    340733  340841  .   +   .   transcript_id "CLUHART00000008717"; gene_id "CLUHARG00000005458";
  scaffold625 maker   exon    341518  341628  .   +   .   transcript_id "CLUHART00000008717"; gene_id "CLUHARG00000005458";
  scaffold625 maker   exon    341964  343277  .   +   .   transcript_id "CLUHART00000008717"; gene_id "CLUHARG00000005458";
  scaffold625 maker   CDS 337915  337971  .   +   0   transcript_id "CLUHART00000008717"; gene_id "CLUHARG00000005458";
  scaffold625 maker   CDS 340733  340841  .   +   0   transcript_id "CLUHART00000008717"; gene_id "CLUHARG00000005458";
  scaffold625 maker   CDS 341518  341628  .   +   2   transcript_id "CLUHART00000008717"; gene_id "CLUHARG00000005458";
  scaffold625 maker   CDS 341964  343033  .   +   2   transcript_id "CLUHART00000008717"; gene_id "CLUHARG00000005458";
  
  ```
  
  while with AGAT you get
  
  ```
  scaffold625 maker   gene    337818  343277  .   +   .   ID CLUHARG00000005458 ; Name TUBB3_2 ; gene_id CLUHARG00000005458
  scaffold625 maker   mRNA    337818  343277  .   +   .   ID CLUHART00000008717 ; Parent CLUHARG00000005458 ; gene_id CLUHARG00000005458 ; transcript_id CLUHART00000008717
  scaffold625 maker   exon    337818  337971  .   +   0   ID "CLUHART00000008717:exon1"  ; Parent CLUHART00000008717 ; gene_id CLUHARG00000005458 ; transcript_id CLUHART00000008717
  scaffold625 maker   exon    340733  340841  .   +   0   ID "CLUHART00000008717:exon2"  ; Parent CLUHART00000008717 ; gene_id CLUHARG00000005458 ; transcript_id CLUHART00000008717
  scaffold625 maker   exon    341518  341628  .   +   2   ID "CLUHART00000008717:exon3"  ; Parent CLUHART00000008717 ; gene_id CLUHARG00000005458 ; transcript_id CLUHART00000008717
  scaffold625 maker   exon    341964  343277  .   +   2   ID "CLUHART00000008717:exon4"  ; Parent CLUHART00000008717 ; gene_id CLUHARG00000005458 ; transcript_id CLUHART00000008717
  scaffold625 maker   CDS 337915  337971  .   +   0   ID "CLUHART00000008717:cds"  ; Parent CLUHART00000008717 ; gene_id CLUHARG00000005458 ; transcript_id CLUHART00000008717
  scaffold625 maker   CDS 340733  340841  .   +   0   ID "CLUHART00000008717:cds"  ; Parent CLUHART00000008717 ; gene_id CLUHARG00000005458 ; transcript_id CLUHART00000008717
  scaffold625 maker   CDS 341518  341628  .   +   2   ID "CLUHART00000008717:cds"  ; Parent CLUHART00000008717 ; gene_id CLUHARG00000005458 ; transcript_id CLUHART00000008717
  scaffold625 maker   CDS 341964  343033  .   +   2   ID "CLUHART00000008717:cds"  ; Parent CLUHART00000008717 ; gene_id CLUHARG00000005458 ; transcript_id CLUHART00000008717
  scaffold625 maker   five_prime_UTR  337818  337914  .   +   .   ID "CLUHART00000008717:five_prime_utr"  ; Parent CLUHART00000008717 ; gene_id CLUHARG00000005458 ; transcript_id CLUHART00000008717
  scaffold625 maker   three_prime_UTR 343034  343277  .   +   .   ID "CLUHART00000008717:three_prime_utr"  ; Parent CLUHART00000008717 ; gene_id CLUHARG00000005458 ; transcript_id CLUHART00000008717
  
  ```
  
  So you can see as example that `Name=TUBB3_2` from the gene feature disappeared with `gffread`.
  
  
  ---
  
  ### Answer by username_2 on 2019-12-29. Score: 5
  
  You can use `gffread` to convert `gff` to `gtf2`, below is from [the manual](http://ccb.jhu.edu/software/stringtie/gff.shtml):
  
  > In order to see the GTF2 version of the same transcripts, the -T
  > option should be added:
  >
  > ```
  > gffread -E annotation.gff -T -o- | more
  >
  > ```
  >
  > The examples above also show that gffread can be used to convert a
  > file between GTF2 and GFF3 file formats.
  
  > **Comments:**
  > **username_0**: Thk for your awnser  
  
  ---
  
  ### Answer by username_3 on 2020-03-17. Score: 1
  
  Actually I started a mini-review about the tools to do such conversion.  
  You can find it here:
  <https://github.com/NBISweden/GAAS/blob/master/annotation/knowledge/gff_to_gtf.md>
  
  As I mentioned earlier they do not behave all the same way...
  
  
  ---
  
  ### Answer by username_4 on 2021-12-21. Score: 0
  
  You can try bioinfokit (<https://github.com/reneshbedre/bioinfokit>) in python.
  
  ```
  from bioinfokit.analys import gff
  
  gff.gff_to_gtf(file="yourfile.gff3") 
  # The converted gtf file will be saved in the same working directory.
  ```
  
  ```
  
  
  ---
  
  