Hi all,
This problem has been addressed here http://seqanswers.com/forums/showthread.php?t=4606. And I noticed that in Cufflinks release 0.9.1, the problem of inconsistent FPKM values returned by cufflinks and cuffcompare had been claimed to be solved. Unfortunately, I inspected the FPKM values of many of the reconstructed transcripts and found they have different FPKM values. I am just curious: is it due to slightly different way of estimating FPKM in cufflinks and cuffdiff? Hope this problem will be eventually solved.
Thanks.
This problem has been addressed here http://seqanswers.com/forums/showthread.php?t=4606. And I noticed that in Cufflinks release 0.9.1, the problem of inconsistent FPKM values returned by cufflinks and cuffcompare had been claimed to be solved. Unfortunately, I inspected the FPKM values of many of the reconstructed transcripts and found they have different FPKM values. I am just curious: is it due to slightly different way of estimating FPKM in cufflinks and cuffdiff? Hope this problem will be eventually solved.
Thanks.
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