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  • Cufflinks - Odd MIR FPKM values.

    Hi all, I'm getting some odd micro RNA FPKM values in my cufflinks output that I'm trying to troubleshoot. The MIRs will show a large FPKM value in one sample, but a zero FPKM in the other samples which seems incorrect. I did some by eye checks in IGV and can't see why this would be.

    Here's an example of what I mean.


    The data in IGV doesn't seem to agree with the FPKM values either. Here's MIR3125 viewed in IGV as an Example.

    Am I maybe missing a cufflinks or tophat option that would avoid this?

    Thanks for any help.

  • #2
    Hi,
    i am sorry to revive that thread but i got the same weird results. In one sample i get FPKM for a transcript and in the other not even tho when i check with IGV i get the same picture as the first sample.

    Im using Cufflinks 2.0.2.

    Thanks for the help

    Comment


    • #3
      It's possible the short length of the MIRs is affecting the FPKM calculation. This thread may be relevant:

      Discussion of next-gen sequencing related bioinformatics: resources, algorithms, open source efforts, etc


      Most importantly, page down to the explanation by Cole Trapnell (one of the authors of Cufflinks).

      Comment

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