strandness of paired-end data

Question

[waqaskhokhar999]

I have used infer_experiment.py from RSeQC and got this output:

This is PairEnd Data
Fraction of reads failed to determine: 0.0659
Fraction of reads explained by "1++,1--,2+-,2-+": 0.0055
Fraction of reads explained by "1+-,1-+,2++,2--": 0.9285

Is it shows that my RNA-Seq data is strand specific and strandness of read1 is opposite with that of gene model, while strandness of read2 is consistent to the strand of reference gene model?

Is that means that its reverse stranded and I have to use s -2 option or s -1 option in featureCounts?

[Joe]

This is not a "Forum" this is a Question type post. I have corrected it for you this time.

[GenoMax]

See this for more info: RSeQC Output from infer_experiment.py - what does it mean?

[erwan.scaon]

See also : Read pair orientation : Illumina TruSeq Stranded mRNA library

Answer 1

[DareDevil]

For dummies, if the output is:

Fraction of reads explained by "1++,1--,2+-,2-+": 0.0055
Fraction of reads explained by "1+-,1-+,2++,2--": 0.9285

You can use -s 2 option for featurecounts

or if the output is:

Fraction of reads explained by "1++,1--,2+-,2-+": 0.9285
Fraction of reads explained by "1+-,1-+,2++,2--": 0.0055

You can use -s 1 option for featurecounts

or if the output is:

Fraction of reads explained by "1++,1--,2+-,2-+": 0.4555
Fraction of reads explained by "1+-,1-+,2++,2--": 0.4585

You can use -s 0 option for featurecounts