Paired-end strand specific RNA-seq

[dekontrol]

Hi all,

I have aligned paired-end RNA-Seq data generated with a strand-specific library (on Illumina HiSeq).

Is possible to known how to assign the pairs to the RNA strand from which was generated from the SAM file?

In other word I am looking for a way to generate two different bigWig files: one with the signal coming from one strand, and one with the signal coming from the other strand..

Thanks very much!

Best,
albert

[Torst]

Did you align them with strand-specific options enabled?

[dekontrol]

I am using an aligner which don't have this option..(novoalign).. However if this is essential I can try other aligners like TopHat..