Transforming stranded RNA-Seq libraries in unstranded
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8.1 years ago

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!

rna-seq stranded • 2.1k views
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It might be worth checking for your condition of interest exactly how much antisense transcription is going on.

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

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8.1 years ago

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

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