I have smallRNA seq data that were produced by poly-adenylating the 3' end prior to PCR amplification. For this reason many of the reads contain the poly-a stretches. But since the sequenced fragments were so short, sometimes the tail is sequenced through and there are nucleotides on the 3' end of the poly-a tail. Like this:
I have used PRINSEQ to remove the poly-a tail, but it seems that it only remove tails at the very end of the sequence. Anyone know how i can remove tails including the following nucleotides like the read above?