About alignment of R1&R2 details in make.contigs()


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.


We do not output the alignments since that would result in a ridiculously large file.