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  • cuffdiff: time-series problem

    Hi all,
    I have RNA-Seq from 3 samples, which can be treated as 3 time-points. And I used cuffdiff to perform the DE analysis. in the isoforms.tracking file, I find the FPKM values for q1, q2, q3. However, I did not obtain 0_1_isoform_exp.diff, 0_2_isoform_exp.diff.. What I got is only a "isoform_exp.diff". Did I make a mistake?
    I used ver0.9.3.
    Command I used was:
    ./cuffdiff -o output_dir -L time1, time2,time3 reference.gtf sample1.sam sample2.sam sample3.sam

  • #2
    i found the answer: cuffdiff integrated all the pair-sample comparisons into a single isoform_exp.diff. It would be great if the manual website could be updated accordingly.

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