Hi all, 

Can someone help me understand the RSeQC Output from infer_experiment.py?

So this is the output:

    This is PairEnd Data
    Fraction of reads failed to determine: 0.0560
    Fraction of reads explained by "1++,1--,2+-,2-+": 0.0192
    Fraction of reads explained by "1+-,1-+,2++,2--": 0.9247

So it's stranded but is it  fr-firststrand or fr-secondstrand? 
I do not understand the help given [here][1]: 

> For pair-end RNA-seq, there are two different ways to strand reads
> (such as Illumina ScriptSeq protocol):
> 
> 1++,1–,2+-,2-+
> 
> read1 mapped to ‘+’ strand indicates parental gene on ‘+’ strand
> 
> read1 mapped to ‘-‘ strand indicates parental gene on ‘-‘ strand
> 
> read2 mapped to ‘+’ strand indicates parental gene on ‘-‘ strand
> 
> read2 mapped to ‘-‘ strand indicates parental gene on ‘+’ strand
> 
> 1+-,1-+,2++,2–
> 
> read1 mapped to ‘+’ strand indicates parental gene on ‘-‘ strand
> 
> read1 mapped to ‘-‘ strand indicates parental gene on ‘+’ strand
> 
> read2 mapped to ‘+’ strand indicates parental gene on ‘+’ strand
> 
> read2 mapped to ‘-‘ strand indicates parental gene on ‘-‘ strand

Thanks for your help!

  [1]: http://rseqc.sourceforge.net
It means you have a standard (dUTP-based) strand-specific library. If you want to use featureCounts, you'll want the `-s 2` setting. For HTSeq-count it's `--strand reverse`.