Cuffdiff multiple accession numbers

[apadr007]

Hello,

I wanted to know why the Cuffdiff "gene.exp.diff" and "cds.diff" files were producing multiple accession numbers in the same row. For example:


XLOC_000122 - - XLOC_000122 AGAP004916,AGAP004918 TSS334,TSS335



As you can tell, this is a single row with two "AGAP" accession numbers, separated by a comma. Why is this happening?

Thanks.

[NM_010117]

This is most likely due to it reporting the different isoforms that are part of that gene. Most mammalian genes have at least two isoforms, if not three or four (or more!). That is why you are also getting two different transcription start sites (TSS): TSS334 and TSS335. One is for AGAP004916 and the other is the transcription start site for AGAP004918.

[apadr007]

This makes absolutely no sense to me. Cuffdiff generates an isoform file so it should simply report isoforms of a particular gene there, not in a file it calls "gene.exp.diff".

I guess it may do with the way isoforms are clumped up into genes. Maybe the algorithm misses some that are very different and therefore calls it a new gene?