Transforming stranded RNA-Seq libraries in unstranded

[elsoja]

I want to detect differential gene expression by comparing two different RNA-Seq libraries, however one of them is stranded and the other one is unstranded. I know that unstranded libraries overrate the expression of RNAs that have a anti-sense transcript.

In order to eliminate this bias, can I align the stranded library in STAR as if it were a unstranded library? Will it eliminate the bias, or there is another factor that introduces a bias that prevents me from comparing these two libraries?

Thank you!

[cmbetts]

I would assume that the comparison would be mostly valid as long as you both align and quantify the stranded library as though it were unstranded. Assuming the stranded library was done with the dUTP method, it amplifies the same fragments as would be present in an unstranded library, just uniformly only amplifying one strand or the other. There still might be some differences if different kits, most likely, or polymerases were used in library construction. If it wasn't done w/ dUTP, the method was probably different enough that it's hard to make the comparison.