Answers.Body: <p>You can get a bit more information by <a href="https://github.com/cole-trapnell-lab/cufflinks/blob/b55bb214ad4abeb58a1435d8f7a7f0dd8bed8b76/src/gff_utils.cpp" rel="nofollow noreferrer">looking at the source code comments</a>. <a href="https://github.com/cole-trapnell-lab/cufflinks/blob/b55bb214ad4abeb58a1435d8f7a7f0dd8bed8b76/src/gff_utils.cpp#L140-L141" rel="nofollow noreferrer">Contained</a> is for single exon transcripts that are primarily contained (<a href="https://github.com/cole-trapnell-lab/cufflinks/blob/b55bb214ad4abeb58a1435d8f7a7f0dd8bed8b76/src/gff_utils.cpp#L145" rel="nofollow noreferrer">>80% overlap</a>) within an exon of an already annotated transcript. <code>Generic exonic overlap</code> is for cases where a transfrag exon overlaps that of an annotated transcript. The strand doesn't seem to matter in such cases.</p>
  
Answers.ContentLicense: CC BY-SA 3.0
Answers.CreationDate: 2017-07-27T12:47:53.153Z
Answers.LastActivityDate: 2017-07-27T12:47:53.153Z
Answers.UserDisplayName: Devon Ryan
Body: <p>Is there any extensive documentation or description for each class of Transfrag class codes as reported by the cuffcompare tool in the Cufflinks package?</p>
  
  <p><a href="http://cole-trapnell-lab.github.io/cufflinks/cuffcompare/#transfrag-class-codes" rel="noreferrer">Official doc</a> might not be the best. </p>
  
  <p>E.g. what does <em>contained</em> mean (class code: c)? Or, what is a <em>generic exonic overlap</em> (class code: o)?</p>
  
Tags: <transcriptome>
Title: Documentation for Transfrag class codes (cuffcompare)
ThreadText: # Documentation for Transfrag class codes (cuffcompare)
  
  (Asked by: username_0 on 2017-07-27)
  
  Is there any extensive documentation or description for each class of Transfrag class codes as reported by the cuffcompare tool in the Cufflinks package?
  
  [Official doc](http://cole-trapnell-lab.github.io/cufflinks/cuffcompare/#transfrag-class-codes) might not be the best.
  
  E.g. what does *contained* mean (class code: c)? Or, what is a *generic exonic overlap* (class code: o)?
  
  **Tags:** transcriptome
  
  
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  ## 1 answers
  
  ### Answer by username_1 on 2017-07-27. Score: 2 | Accepted answer
  
  You can get a bit more information by [looking at the source code comments](https://github.com/cole-trapnell-lab/cufflinks/blob/b55bb214ad4abeb58a1435d8f7a7f0dd8bed8b76/src/gff_utils.cpp). [Contained](https://github.com/cole-trapnell-lab/cufflinks/blob/b55bb214ad4abeb58a1435d8f7a7f0dd8bed8b76/src/gff_utils.cpp#L140-L141) is for single exon transcripts that are primarily contained ([>80% overlap](https://github.com/cole-trapnell-lab/cufflinks/blob/b55bb214ad4abeb58a1435d8f7a7f0dd8bed8b76/src/gff_utils.cpp#L145)) within an exon of an already annotated transcript. `Generic exonic overlap` is for cases where a transfrag exon overlaps that of an annotated transcript. The strand doesn't seem to matter in such cases.
  
  
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