Answers.Body: <p>I think the part of the code that should allow you to do this is in <code>chromomer.cc</code>.</p>
  
  <p>Lines 2857-2983 form the function <code>parse_command_line</code>. Nowhere is there any reference to anything resembling parsing a GFF file, so I think the documentation is not in line with the code at this point.</p>
  
  <p>For reference, I looked at version 1.07. It would be helpful if the code were on github.</p>
  
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Answers.CreationDate: 2018-01-20T10:58:15.357Z
Answers.Text: The distribution of Chromonomer comes with a script for translation.
Answers.UserDisplayName: Tássio
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Answers.CreationDate: 2017-10-26T06:47:59.880Z
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Body: <p>I am trying to use <a href="http://catchenlab.life.illinois.edu/chromonomer/" rel="nofollow noreferrer">Chromonomer</a>. It should be possible (according to the software page and a paper) to add a GFF/GTF file to the analysis.</p>
  
  <p>Alas, neither the built-in help nor some light source code browsing were enough to find a way of passing the file to the software.</p>
  
  <p>How can I use a GFF or a GTF file with Chromonomer?</p>
  
Tags: <gff3><gtf>
Title: How to provide a GFF/GTF file to Chromonomer
ThreadText: # How to provide a GFF/GTF file to Chromonomer
  
  (Asked by: username_0 on 2017-10-19)
  
  I am trying to use [Chromonomer](http://catchenlab.life.illinois.edu/chromonomer/). It should be possible (according to the software page and a paper) to add a GFF/GTF file to the analysis.
  
  Alas, neither the built-in help nor some light source code browsing were enough to find a way of passing the file to the software.
  
  How can I use a GFF or a GTF file with Chromonomer?
  
  **Tags:** gff3, gtf
  
  
  ---
  
  ## 1 answers
  
  ### Answer by username_1 on 2017-10-26. Score: 1
  
  I think the part of the code that should allow you to do this is in `chromomer.cc`.
  
  Lines 2857-2983 form the function `parse_command_line`. Nowhere is there any reference to anything resembling parsing a GFF file, so I think the documentation is not in line with the code at this point.
  
  For reference, I looked at version 1.07. It would be helpful if the code were on github.
  
  > **Comments:**
  > **username_0**: The distribution of Chromonomer comes with a script for translation.  
  
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