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Old 12-09-2010, 02:09 PM   #1
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Location: USA

Join Date: Aug 2010
Posts: 103
Default Different FPKM values of cufflinks and cuffdiff

Hi all, sorry for repeatedly posting the same question. But I am still confused about the different FPKM values returned by cufflinks and cuffdiff. Did I make mistakes in one of the steps? Below is how I use the package:

1)run cufflinks on the sam files obtained by Tophat
2)run cuffcompare on the gtf files in last step, I used UCSC known genes as the reference. And I got the stdout.combined.gtf and the tracking files as expected.
3)using the stdout.combined.gtf obtained in 2) as reference, I run cuffdiff on the sam files of the samples and obtained the *.diff and *.tracking files.

However, I found that for many isoforms (from isoforms.tracking), their FPKM values from the samples usually do not match those values by cufflinks from step 1). The version I used is 0.9.2.

Could anybody help to explain this? And, what is the reason to re-assign the reads to transcript and re-estimate abundance in cuffdiff?

I desperately look forward to your answers. Thank you all.
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