I’m very very new to analyzing pyrosequencing results. I’m starting to understand how trimming etc. works. A colleague suggested comparing my mothur results to the RDP pyrosequencing pipeline results and here’s where I’m really stuck.
For some reason, although I’m starting with the same fasta file, when I use “trim.seqs” in mothur and use “minlength” and “maxlength” to trim sequences, it gives me a different result then when I set the same initial parameters in RDP. Does anyone have any insight into this?