Using PolyA+ to identify/quantify lncRNAs?

[warrenemmett]

Hi,

In some recent publications I have seen people quantifying lncRNA using polyA+ data (this is from primary data generated for the study). As far as I'm aware there are lncRNA that have polyA tails but surely you're biasing your analysis by ignoring a significant fraction which do not have polyA tails. Just curious if there is a reason for this that I am not aware of.

Thanks!

[rkizen]

I think it's just to remove a level of uncertainty. With poly A selection you can get strand information and have some verification of capturing the 3' end of the transcript. Otherwise it is almost impossible to know if the predicted transcript is not just a degraded mRNA.