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  • Different fpkm values for cuffdiff and cuffcompare

    Hi,

    I have noticed that some of my FPKM values are 0 in the gene_exp.diff file.I did notice that it was not 0 in the transcripts.tmap file.Does anyone know why does this is happening.

    Thanks,
    Joji

  • #2
    hi did find an answer to this?

    thanks,
    ib

    Comment


    • #3
      I have the same problem, anybody has a clue?

      Comment


      • #4
        You'd have to ask the authors about this one. I'm not sure why their expression assignment algorithm would make different decisions when cufflinks is run verses when cuffdiff is run.
        /* Shawn Driscoll, Gene Expression Laboratory, Pfaff
        Salk Institute for Biological Studies, La Jolla, CA, USA */

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