I am trying to learn what my options are if I would like to trim polyA from my reads. (FastqC repo see previous discussion: https://www.biostars.org/p/302411/#302507) We are quite certain we need to trim adapter, which we would use bbduk, but we also see polyA showing in many reads, and would like to trim that too.
Since polyA shows in different reads with different length, it does not make sense to trim by length. I hope to trim all the way till the nucleotide is not A. Any suggestions?
(Or maybe I should just go ahead with alignment (Tophat) and let the aligner ignore polyA in the reads?)
Thank you very much!