I am working with featureCounts and got a bit confused by -s parameter. I have strand specific RNAseq data. So, I guess my option for -s would 1 but why would somebody use 2 (reversely stranded)?
-s <int> Indicate if strand-specific read counting should be performed.
It has three possible values: 0 (unstranded), 1 (stranded) and
2 (reversely stranded). 0 by default.
Hi,
It depends on the library used in the sequencing protocol. There is a wide range of library types : ff-firststrand, ff-secondstrand, ff-unstranded, fr-firststrand, fr-secondstrand, fr-unstranded ... A read and its mate will not map to the genome in the same way according to the library stranding.
As featureCounts cares about the stranding of a read, it is important to specify the correct -s parameter.
PS: I know it might be a bit off topic, but this manual page from sailfish provides a nice overview of the ways a read and its mate can map on the genome according to libraries.
I checked my data with infer_experiment.py script, inside RSeQC package and found out following configuration. Does it mean that I have to use -s2 for featureCounts and I have fr-secondstrand?
2. +-,-+
- read mapped to '+' strand indicates parental gene on '-' strand
- read mapped to '-' strand indicates parental gene on '+' strand
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