Consensus on poly-a selected lncRNAs for differential expression analysis

Question

[bart]

Hi all,

This is somewhat related to my previous question: I was wondering if there is a general consensus on the validity of poly-a selected lncRNAs for DEA. Would this have scientific value? Or would it always be better to perform whole transcriptome sequencing for something like DEA of lncRNAs?

Thanks!

Answer 1

[Carlo Yague]

Some lncRNA are polyadenylated, others are not. If you want to analyse all lncRNA, it is best to perform whole (or ribodepleted) transcriptome sequencing. That being said for the lncRNA for which there is sufficient signal in poly(a)-seq data, you can still perform DEA while keeping in mind the limitation that you might be missing some non-poly(a) expression signal.