Dear mothur community,
I am completely new to mothur and have so far been processing my MiSeq data according to the MiSeq SOP (by the way, great job there!). I was able to assign a taxonomy to OTUs retrieved from 16 samples via the classify.otu command. However, what I need now is to reassign those OTUs and taxonomies to the corresponding samples, preferrably creating a new file for each of the 16 samples containing the list of OTUs, size and taxonomy. I couldn’t really deduce how to do this from the SOP guide, as it starts with analysis of diversity etc. after the classification, which I don’t need for the time being (for now I’d just like to look at the OTUs of each sample and compare).
Which command should I use? I was thinking of the get.otus, maybe like this?
mothur > get.otus(groups=1, group=enrichment.contigs.good.groups, list=enrichment.trim.contigs.good.unique.good.filter.unique.precluster.pick.pds.wang.pick.pick.tx.list)
Please consider I’m completely new to all of this. It might have been a dumb question to start with, but right now I cannot find a solution to my problem.