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Old 01-05-2016, 12:24 AM   #1
Location: Berlin

Join Date: Nov 2011
Posts: 11
Default interpretation of results of RSeQC for cuffdiff and featureCounts

I have RNAseq data from encode mouse and to do some analysis with cuffdiff and featureCounts I need first to understand what library type I have to chose the right parameters for cuffdiff and featureCounts.

I ran from RSeQC and found out following configuration:

This is SingleEnd Data

Fraction of reads failed to determine: 0.0023

Fraction of reads explained by "++,--": 0.0160

Fraction of reads explained by "+-,-+": 0.9817

So, I need to specify -library-type for cuffdiff. If I interpreted it right I have fr-secondstrand. Is it correct?
For featureCounts I need to specify -s parameter. It would be -s2, is it correct?

-s <int>      Indicate if strand-specific read counting should be performed.
                  It has three possible values:  0 (unstranded), 1 (stranded) and
                  2 (reversely stranded). 0 by default.
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