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  • fuad193
    Member
    • Feb 2012
    • 17
    #1

    Cufflinks FPKM is different than Cuffdiff FPKM !!

    Why I get different FPKM values if I run a BAM file on cufflinks alone and on cuffdiff against another BAM file ? Aren't FPkM values consistant irrespective to whether it comes from cufflinks or cuffdiff ?

    What should I do now, consider cuifflinks FPKM or cuffdiff FPKM ? I mainly want to compare samples in time series and on WT vs mutant. Any suggestions ?

    Edited: MY main purpose is to find the half life of each Transcripts RNA, so I want to construct a plot of log(FPKM) vs time. Which FPKM should I use ?!
    Last edited by fuad193; 04-12-2013, 12:51 AM.
    Tags: cuffdiff, cufflinks, fpkm, rna-seq
  • NGSfan
    Senior Member
    • Apr 2009
    • 181
    #2
    Originally posted by fuad193 View Post
    Why I get different FPKM values if I run a BAM file on cufflinks alone and on cuffdiff against another BAM file ? Aren't FPkM values consistant irrespective to whether it comes from cufflinks or cuffdiff ?

    What should I do now, consider cuifflinks FPKM or cuffdiff FPKM ? I mainly want to compare samples in time series and on WT vs mutant. Any suggestions ?

    Edited: MY main purpose is to find the half life of each Transcripts RNA, so I want to construct a plot of log(FPKM) vs time. Which FPKM should I use ?!
    Please find my solution in this thread http://seqanswers.com/forums/showthread.php?t=26041. The problem is that the default settings between cufflinks and cuffdiff are different.



    btw- there is a new version of cufflinks/cuffdiff 2.1.1 with some bug fixes, although I haven't tested that they have fixed the default setting of the multi-frag-hits (reported as unlimited but actually set to 1 in 2.0.2)
    Last edited by NGSfan; 04-16-2013, 07:12 AM.

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