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 infer_experiment.py 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.