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  • jmwhitha
    replied
    I take that back, actually I changed the max-bundle-frags to 70X the default.

    Please, if anyone knows why my p-values are defaulting to one and my test_stat is defaulting to 0, I would greatly appreciate the information.

    Thank you!

    Leave a comment:


  • HIDATA to LOWDATA status and now false p value Cuffdiff isoform_exp.diff

    Hello SeqAnswers community,

    When I first tried to run cuffdiff, I found that I had many HIDATA status for my isoform_exp.diff. After running it with 10X the default max-bundle-frags, I didn't have any HIDATA status left. However, I have many LOWDATA status now.

    It's very strange. I am looking at a particular gene right now that has 167095 count but has a LOWDATA status while the same gene in the other condition has a OK status (821 count). Before adjusting the max-bundle-frags, they both had HIDATA.

    Clearly, there is differential expression, but cuffdiff isoform_exp.diff says "no".
    test_id = TCONS_00000809
    gene_id = XLOC_000295
    gene = Doesn't matter
    locus = Doesn't matter
    sample_1 = Cond1
    sample_2 = Cond2
    status = LOWDATA
    value_1 = 7012.28
    value_2 = 1.07803
    log2(fold_change) = -12.6673
    test_stat = 0
    p_value = 1
    q_value = 1
    significant = no

    Why is it giving these high p and q values?

    Thank you and God bless,
    Jason

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