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Old 05-09-2011, 09:26 PM   #20
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Location: India

Join Date: Feb 2011
Posts: 7

Originally Posted by adarob View Post
The multiple FPKM problem occurs when genes have transcripts that do not overlap with any other transcripts in the gene. For example, this occurs in the ENSG00000125388 gene from ENSEMBL/hg19. We are aware of this issue and will eventually change the behavior, but for now a simple solution is just to sum the FPKMs since the gene FPKMs are just the sum of the transcript FPKMs anyways. The issue should not occur in Cuffdiff.

I would not draw any conclusions about the FPKM of the FAILED genes.
Does this mean that I will have to download the cuffcompare file, edit it, upload it on galaxy and then run cuffdiff on this gtf file? Thanks for your help!
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