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Old 04-26-2017, 11:18 PM   #2
sdriscoll
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Location: San Diego, CA, USA

Join Date: Sep 2009
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first of all let me say that I agree with your interpretation. the third transcript does not overlap the first two and it has given all three the same 'gene_id' value.

the only thing that comes to mind is that the assembly from stringtie, or cufflinks for that matter, is an attempted explanation, and often a simplification, of the alignment data. you may learn more about this by looking at the alignments in an alignment browser such as UCSC or IGV.

while i doubt this, stringtie could be very, very smart and have assembled the third isoform from reads that multimapped between it and the first two transcripts which would imply they are all the same gene but one that is repeated in more than one position.
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/* Shawn Driscoll, Gene Expression Laboratory, Pfaff
Salk Institute for Biological Studies, La Jolla, CA, USA */
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