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  • Cuffdiff output isoform_exp.diff - multiples of same transcripts

    I've been going through the various cuffdiff output threads, but I can't find the answer i'm looking for. Here goes - thanks in advance for your help

    I ran cufflinks (RABT mode) -> cuffmerge with GTF -> cuffdiff

    Now I want to know which isoforms are differentially expressed. As far as I can understand, there are 4 things relevant to this:

    isoforms.fpkm_tracking
    isoforms_counts_tracking
    isoform_exp.diff file
    splicing.diff

    The tracking files have transcript names while the isoform_exp.diff file doesn't, so I map the transcript names over according to the TCONS (whatever that may be).
    I presumed that each line in isoform_exp.diff would correspond to one transcript, but that's not the case. There are multiple lines with the same transcript name, which have different fold change values. So how do I get a single fold change and confidence per transcript? Isn't that was isoform-centric analysis is supposed to produce?

    The splicing.diff file has fewer lines, but in it, all the lines say NOTEST (even ones that were OK in the isoform_exp.diff

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