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  • Cufflinks gene FPKM different in genes.fpkm_tracking vs isoform.fpkm_tracking

    Hello,

    I am worried to see different values of FPKM for the same gene in the Cufflinks genes.fpkm_tracking vs isoforms.fpkm_tracking files.

    I was under the impression that one could use the genes.fpkm file if we are not worried about the isoform information. Am I wrong?

    Please see example below:

    login3$ grep Nox1 genes.fpkm_tracking
    ENSMUSG00000031257.8 - - ENSMUSG00000031257.8 Nox1 - chrX:134086420-134221956 - - 2.56323 2.26375 2.71812 OK

    login3$ grep Nox1 isoforms.fpkm_tracking |grep -v ENSMUST
    ENSMUSG00000031257.8 - - ENSMUSG00000031257.8 Nox1 - chrX:134086420-134221956 135536 0.0626628 0.00383565 0.00300087 0.00468318 OK


    Could someone (especially developers) please comment?

    Thanks,
    Manoj.

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