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Old 02-09-2011, 07:58 AM   #1
madsaan
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Question 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
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Old 10-14-2012, 12:33 AM   #2
IBseq
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hi did find an answer to this?

thanks,
ib
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Old 12-12-2012, 08:54 AM   #3
sqcrft
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I have the same problem, anybody has a clue?
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Old 12-12-2012, 05:14 PM   #4
sdriscoll
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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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