Question: Transforming stranded RNA-Seq libraries in unstranded
gravatar for elsoja
4.4 years ago by
elsoja120 wrote:

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!

stranded rna-seq • 1.3k views
ADD COMMENTlink modified 2.2 years ago by Biostar ♦♦ 20 • written 4.4 years ago by elsoja120

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

ADD REPLYlink written 4.4 years ago by fanli.gcb690

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

ADD REPLYlink written 4.4 years ago by elsoja120
gravatar for WouterDeCoster
4.4 years ago by
WouterDeCoster44k wrote:

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

ADD COMMENTlink written 4.4 years ago by WouterDeCoster44k
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