Strandedness wrong for Cufflinks quantification
lweasel opened this issue · comments
In quantifiers.py, Cufflinks quantification is currently using "--library-type fr-unstranded" for TopHat, but "--library-type fr-secondstrand" for Cufflinks itself. These should be the same - fr-secondstrand presumably, because we're claiming that FluxSimulator outputs stranded reads when the UNIQUE_IDS option is set.