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cuffdiff not strand-specific?

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  • cuffdiff not strand-specific?

    Hi,

    regardless which --library-type I specify, I get always the same FPKM results with cuffdiff. Contrary cufflinks seems to give strand specific results. All cuffdiff FPKMs correlate best with unstranded cufflink's FPKMs (--library-type=fr-unstranded). Is cuffdiff not strand specific?

    Thanks & best regards,
    Thomas
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