Question: strandness of paired-end data
0
gravatar for waqaskhokhar999
10 months ago by
waqaskhokhar99960 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 • 548 views
ADD COMMENTlink modified 8 months ago by Biostar ♦♦ 20 • written 10 months ago by waqaskhokhar99960

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

ADD REPLYlink written 10 months ago by jrj.healey13k

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

ADD REPLYlink written 10 months ago by genomax70k

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

ADD REPLYlink written 10 months ago by erwan.scaon720
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