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Old 11-15-2010, 11:30 AM   #1
burkard
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Location: Vienna

Join Date: Jul 2010
Posts: 2
Default 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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