Currently, I run through some PE250 reads from MiSeq. It works fine. Since base quality on my R2 at 3’ is pretty bad, and I would like to see how do R1 and R2 aligned to each other during make.contigs() step. But I couldn’t see the alignment output from make.contigs().
Is it possible to check R1 and R2 alignment using mothur command or other ways?
Thank you very much in advance.