I’ve narrowed down to 19 OTUs that I want to look at. I was wondering if there was any way to get the sequences that were used to make up the OTU out, organised by sample they originate from? I have managed to do it so that I get them out but not so that I can see which samples those sequences initially came from?
If you already have the unique sequences that were used to form the OTU, I would just use the get.seqs command on your pre-OTU count table. That would reduce the count table down to just the sequences you’re interested in, and would maintain the group distribution information (it would also have the nice side effect of removing any groups that didn’t contain the sequnces).