rna seq single ended -Information on Rseqc report
Entering edit mode
2.8 years ago
ASid ▴ 10

I am newbie for ngs data analysis and so my questions would be very naive. With a lot of struugle I could use infer_experiment.py of rseqc to infer the stranded ness of the single ended publicly availaible dataset data that I was using. The output is displayed as follows:

This is SingleEnd Data Fraction of reads failed to determine:0.0198 
Fraction of reads explained by "++,--": 0.4819 
Fraction of reads explained by "+-,-+": 0.4982

So can anybody help me in interpreting it that it is stranded or unstranded and how we would guess that? 2. I use hisat2 for alignment and there was an option about strandedness and I used unstranded so it should be fine righht ?

rna seq Rseqc Standedness • 750 views
Entering edit mode
2.8 years ago
lshepard ▴ 460

This is unstranded RNAseq. You can tell by the almost equal distribution of reads explained by forward and reverse output.


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