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  • RNA-Seq - From Cufflinks FPKM to differential gene expression

    Hello,

    I recently started working with RNA-Seq. I have a study with 8 samples divided in 2 groups (let say A and B). I applied the tophat-cufflinks pipeline. As a result, for each file, i have "genes.fpkm_tracking" which contains the fpkm for each read.

    The question is : is it possible to estimate the differential gene expression between these 2 groups based only on these fpkm results.

    (i read a post from Simon Anders where i think he was suggesting that this is impossible. but this post was old and anyway i can't find it again).

    If not, what is the point of using Cufflinks?

    thanks

  • #2
    Hi Aituka,
    CUFFLINKS output is used as INPUT for cuffdiff, which anlayses the fpkm values betwseen the samples to give you differential expression. alternatively u can use a refence annotation rather than cufflinks, but cuffdiff requires certain attributes which the reference annotation does not have

    hope it helps.
    ib

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