alternative polyadenylation in RNA seq data

Question

[shrinka.genetics]

From RNA seq data is it possible to have an idea about "alternative polyadenylation"??? As per my knowledge is concerned during library preparation "riboreduction" is used as enrichment strategy. In that process does poly A entail remain there when we get the FASTQ file?

Answer 1

[jared.andrews07]

I don't know what you mean by "alternative polyadenylation".

Yes, you will still see polyA adenylation after performing ribosomal RNA depletion. There are two common strategies for getting rid of ribosomal RNA during RNA-seq - ribosomal RNA depletion (where the ribosomal RNA is removed) and polyA selection (where RNA molecules with polyadenylated tails are isolated). The former method will retain RNA molecules with and without polyadenylation (some lncRNAs do not have polyA tails), while the latter will retain only RNA molecules with polyA tails (thereby removing the previously mentioned lncRNAs in addition to rRNA).