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  • Unknown definitions of instances output by CummeRbund

    Hi all,

    Now I am trying to analyze the results of differential expression tests using CummeRbund. I simply loaded the output files of Cuffdiff into CummeRbund. And I got some basic statistics as follows.

    CuffSet instance with:
    8 samples
    14712 genes
    15339 isoforms
    14950 TSS
    14726 CDS
    102984 promoters
    104650 splicing
    100184 relCDS
    Here I am wondering why the instance numbers of TSS and promoters are different, as well as CDS and relCDS? If it is due to their different notions, what could they be used for, especially "promoters", "splicing" and "relCDS"?

    Any explanations?

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