How to access if RNA-seq data is strand-specific?

Question

[JJ]

Hi everyone,

I would like to access if RNA-seq data is strand-specific. I came across RSeQC which can access this. Do you have any other suggestions for tools which can do this? Any advice is very much appreciated.

Thanks

[h.mon]

RSeQC infer-experiment-py is pretty good for this purpose, just go ahead and use it. QoRTs also can determine strand-specificity, but infer-experiment.py is more straightforward to use.

Answer 1

[swbarnes2]

If you align your data with STAR aligner, it can output read per gene, and it does so three different ways,; assuming the protocol is unstranded, assuming your reads should align in the forward direction, assuming they should align in the reverse direction. So you can see which column has the most reads aligning best.

[sbcrg]

Hi,

If the column corresponding to the "reverse" (fr-firststrand) has very low number of reads assigned, and the "pos" (fr-secondstrand) column has a number of reads comparable to the "non stranded" column, can I assume/conclude the experiment is "pos" (i.e. stranded but the opposite way as for the standard Illumina TruSeq RNA-seq protocol)?

Here are the counts of reads assigned I have for a couple of samples (single end RNA-seq) to illustrate this:

sample reverse yes no

sample1 88,171 3,585,710 3,561,601

sample2 77,863 3,143,859 3,119,066

Thanks!