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  • cuffdiff - the -c parameter

    Hello,

    I'm running cuffdiff for DE.

    I'm running with -c parameter as 10. I'm gettig test OK, while the raw counts at that locus are lower than 10.
    I have two conditions: con_1 have 2 replicates, and con_2 have one replicate.

    The raw counts for con_1 are:
    0 for the first replicate
    3 for the second replicate
    The raw count for con_2 is: 2

    I can't understand why the test is OK. isn't it should be NOTEST in that case?

    one more question: how does cuffdiff treat replicates in a condition to set the status of the test? does it sum all the raw counts and compare the sum to the -c parameter? Does it do something alse?

    Thanks,
    Maya

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