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  • Xinlitik
    Junior Member
    • Nov 2012
    • 7
    #1

    Using cuffdiff for isoform DE

    After running CuffDiff on my two conditions, I have the differential expression for various isoforms of genes in isoforms_exp. I would like to determine which isoforms are actually involved (ie the sequence of the alternate transcript) but I can't figure out how to get that information. The only identifying difference I can see between isoforms is the internal ID used by cufflinks, so it seems like that would be the key, but I don't know how to translate the internal ID into useful information in a genome browser, for instance.

    Does anyone know how this can be done? Thanks
    Tags: None
  • tlifeyu
    Junior Member
    • Mar 2011
    • 1
    #2
    Cuffcompare may be used compare with reference annotation.

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