Question about RNA-seq read strand

[harrike]

Hi All,

I downloaded a few public RNA-seq data, and mapped them to the genome and viewed in IGV . As I don't know if the libraries were constructed strand-specifically. Is it possible to judge whether the data are strand-specific or not from the alignment (see an example figure below)? I feel it is (but would like to confirm). Because almost all the genes are of reads of the same direction.

Thanks,

Rui

[GenoMax]

See the discussion in a thread from this morning: http://seqanswers.com/forums/showthread.php?t=66241

[harrike]

Hi GenoMax,

Thanks for your reply. Somehow I am not able to install the RSeQC.

I referred to this thread --- "http://seqanswers.com/forums/showthr...of-pair+strand". My alignment look exactly like what was mentioned in it.

Rui