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  • Cuffdiff outputs mostly FAIL

    Hi,

    I used TopHat on two short-read SOLiD samples, then cufflinks with refFlat as my GTF, then cuffcompare to find differences between the samples. I'm looking for splicing differences, however in splicing.diff I could find no entry with a test status of OK (most were FAIL). What causes this? Is there a way to fix this?

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