Statistics About Poly-A Tails In Rnaseq Reads

Question

[Stroehli]

Hi, I want to get information about the amount and average length of Poly-A tails in my RNAseq reads. Is there any tool that performs this? Preferably in a time efficient manner, because I have around a billion 100bp SE-reads. If I happen to find a lot of Poly-A in my reads, how can I best trim them?

I looked at RNA-SeQC but it doesn't seem to give any statistics about Poly-A tails.

Stroehli

Answer 1

[Devon Ryan]

If a read is all or almost all poly-A then it probably won't align anyway. If you're OK with not going through the entirety of the dataset, fastQC will let you know how much A (or AAAAA, since I think it uses pentamers) enrichment you have in your reads. I've not personally had any issues with too much polyA in the reads, but you could always use any read trimmer and just tell it to trim AAAAAAA, or something like that, from the 3' end.