Transforming stranded RNA-Seq libraries in unstranded

Question

[Antonio Camargo]

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!

[fanli.gcb]

It might be worth checking for your condition of interest exactly how much antisense transcription is going on.

[Antonio Camargo]

I'm filtering for lincRNAs in both libraries and them I'll check differential expression for each lincRNA.

Answer 1

[WouterDeCoster]

As the library preparation of the two sets is different such a comparison would likely be invalid.