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  • rboettcher
    Member
    • Oct 2010
    • 71
    #16
    Hi Alexandra,

    Just to show that you are not alone with your experiences:

    cufflinks 2.0.1
    http://seqanswers.com/forums/showthread.php?t=21824

    cufflinks 1.3
    http://seqanswers.com/forums/showthread.php?t=21020

    I'm currently running another analysis using cufflinks 2.0.2, but I do not expect the results to differ.
    Therefore, I am in the process of switching to edgeR and DEXSeq for DE and AS analysis which already produces results close to the ones obtained via CLC Bio.

    I'm only using cufflinks for transcript assembly of certain regions now, as in my opinion the abundance estimation is not usable for larger sample groups.

    Cheers

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