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  • cummeRbund / cuffdiff output

    I aligned RNAseq reads and ran cuffmerge then cuffdiff on the transcripts.gtf file, with a mouse genome annotation from UCSC.

    Everything works and seems correct.

    When I analyze the results using CummeRbund, i get
    CuffSet instance with:
    2 samples
    99458 genes
    136223 isoforms
    112151 TSS
    24701 CDS
    99458 promoters
    112151 splicing
    20273 relCDS


    This is my first time working with mouse data, but why are there so many genes? This doesn't seem right. Should be like 17K genes ... Does anyone know what's going on?

    There are a total of 6 samples here, that are grouped as two samples in cuffdiff.

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