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  • #1

    cufflinks version 2.0.2 vs 1.3.0

    Hi, I compared the latest version cufflinks 2.0.2 with previous results obtained from 1.3.0 and the results are completely different. I have 2 biological replicates for each condition and the number of differentially expressed genes drops from more than 3000 to 200.
    How can I evaluate the results?
    Although the old version could be yielding false positives, this new version seems highly stringent.
    Any suggestions on how to analyze the results?
    Thanks!
    Tags: None
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