Question: strandness of paired-end data
0
gravatar for waqaskhokhar999
6 months ago by
waqaskhokhar99910 wrote:

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?

rna-seq featurecounts • 394 views
ADD COMMENTlink modified 4 months ago by Biostar ♦♦ 20 • written 6 months ago by waqaskhokhar99910

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

ADD REPLYlink written 6 months ago by jrj.healey12k

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

ADD REPLYlink written 6 months ago by genomax65k

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

ADD REPLYlink written 6 months ago by erwan.scaon670
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