Our organisms have polymorphic DNA (multiple genomes per individual organism). For this reason primers are never 100% specific, even for highly conserved genes. I have noticed that I can eliminate all non-target sequences if I filter out anything that has less than a 70% match at the order level, against our somewhat limited database. Is there a way to induce MOTHUR to filter those out after a cluster split, rather than doing so manually?
Well… you could use a threshold of 70% in classify.seqs and then I think you could use remove.lineage where the taxon is “unclassified;unclassified;unclassified;”
See if that works.
Pat