Polyadenylation cleavage sites detection from rRNA-depleted RNA-Seq

Question

[Nicolas Rosewick]

Hi,

I try to detect specific polyadenylation cleavage site in my RNA-Seq data. Anyone has tried that using rRNA-depleted RNA-Seq (2x100bp). Is there sufficient polyA supporting reads ? I know it was done using polyA-enriched RNA-Seq (http://www.nature.com/nature/journal/v464/n7289/full/nature08872.html) but I didn't find anything on rRNA-depleted RNA-Seq. My first idea was to align R1 and R2 separtely using STAR allowing a lot of soft-clipping.

Any advice ?

Thanks

[Chirag Nepal]

Just my thought: I think RNA-seq does not have high resolution to provide information about poly adenylated cleavage site at single nucleotide resolution. For such info, 3P-seq, poly-A-seq is used, couple of papers from 2014.