<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>

CC BY-SA 3.0
2018-01-20T10:58:15.357Z
The distribution of Chromonomer comes with a script for translation.
Tássio
CC BY-SA 3.0
2017-10-26T06:47:59.880Z
2017-10-26T06:47:59.880Z
holmrenser
<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>

<gff3><gtf>
How to provide a GFF/GTF file to Chromonomer
# 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

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## 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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