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  • 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 infer_experiment.py from RSeQC and found out following configuration:


    Code:
    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?




    Code:
    -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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