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Old 02-27-2014, 10:00 PM   #15
Simon Anders
Senior Member
Location: Heidelberg, Germany

Join Date: Feb 2010
Posts: 994

Overlapping genes on the same strand cannot be distinguished in principle -- at least not by reads that map to the overlapping part. So, if the overlap is small, these will only be a few read, and you could ignore the issue. If, however, the overlap is big, you should consider the two genes as different isoforms of the same gene, and hence give them the same name.

So, I would somehow edit the GTF file such that whenever there are two genes A and B with large overlap, you replace all occurances of the gene IDs "A" and "B" with something like "A+B".
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