RSeQC infer_experiment output interpretation to infer library type fr-firstand or fr-secondstrand
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18 months ago
nlehmann ▴ 130

Hello,

I am doing some analysis of single cell RNA-seq data from 10xGenomics (protocol). I wanted to infer the library type to I ran RSeQC infer_experiement and got this result:

This is SingleEnd Data
Fraction of reads failed to determine: 0.0978
Fraction of reads explained by "++,--": 0.8156
Fraction of reads explained by "+-,-+": 0.0867

Refering to RSeQC documentation, I concluded that we have here SE-like data (10xGenomics data is actually PE but read 1 is used only to keep some barcoding of the cells) and it's stranded. So strandness of reads is concordant with strandness of reference gene.

Now I want to know if we have fr-firstand or fr-secondstrand data. By reading these posts, A: Infer-experiment.py, is strand-specific? and RSeQC infer_experiment.py results interpretation for cuffdiff and featureCounts, I could assume that for SE data, stranded = fr-secondstrand (majority of "++,--") and reversly stranded = fr-firststrand (majority of "+-,-+").

Is it a correct interpretation or did I miss something ?

RNA-Seq RSeQC annotation • 473 views
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