Question on directional and non-directional RNA-seq

[trombidu]

Hi,

I would like to get some RNA-seq data from NCBI to test our method, but I am not sure the given data are strand-specific or not. How can we know that, please?

Thank you very much.

[Dario1984]

It is not very rigorous, but you can download the mapped data, load it into a genome browser, then look at some highly expressed known genes. Do you see many reads in both directions, or almost all reads in one direction ?

[dietmar13]

RSeQC

RSeQC checks for strand specificity...

http://code.google.com/p/rseqc/

[trombidu]

Thanks a lot.
Mapped data are not always available. So we look for kind of keywords which imply strand specificity.
A tool like RSeQC does help.