text: user294: 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 might not be the best. 
  E.g. what does contained mean (class code: c)? Or, what is a generic exonic overlap (class code: o)?
  
  user77: You can get a bit more information by looking at the source code comments. Contained is for single exon transcripts that are primarily contained (>80% overlap) 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.
  
original_text: 294: <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>
   77: <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>
  