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  • lucasmiguel
    Junior Member
    • Jul 2014
    • 9
    #1

    Cuffdiff - NO TESTED isoform

    Hi !
    I have one question. Analysing one gene differentially expressed by Cuffdiff, i saw that all of your isoforms are not differentially expressed. BUT the isoform that makes the gene be differentially expressed is NOT TESTED ( your FPKM is the highest in comparison of others isoforms ).

    My question is: Cuffdiff removes the highly expressed isoforms and after testing them, he sum all FPKM of all isoforms for analyze the gene?

    this explain why i have genes differentially expressed with no one isoform differentially expressed, right?

    Thanks to all.
    Tags: cuffdiff, deg, fpkm, isoforms, testing expression
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