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
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