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-   -   Different fpkm values for cuffdiff and cuffcompare (http://seqanswers.com/forums/showthread.php?t=9351)

madsaan 02-09-2011 07:58 AM

Different fpkm values for cuffdiff and cuffcompare
 
Hi,

I have noticed that some of my FPKM values are 0 in the gene_exp.diff file.I did notice that it was not 0 in the transcripts.tmap file.Does anyone know why does this is happening.

Thanks,
Joji

IBseq 10-14-2012 12:33 AM

hi did find an answer to this?

thanks,
ib

sqcrft 12-12-2012 08:54 AM

I have the same problem, anybody has a clue?

sdriscoll 12-12-2012 05:14 PM

You'd have to ask the authors about this one. I'm not sure why their expression assignment algorithm would make different decisions when cufflinks is run verses when cuffdiff is run.


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