I’m sure I’m missing something obvious here, but I have not found an answer that works for my specific situation. I am wanting to remove OTUs that are unclassified at anything above a family level.
I have used this code, but I am not sure how to get the filter down to a finer resolution without knowing specifically which phyla, orders, or families to put into the code:
This creates a file called unclassified.accnos that has the listing of sequences that are unclassified. You can then use this within the remove.seqs command from within mothur along with your current fasta, count_table, and taxonomy files (i.e. the ones parallel to stability.trim.contigs.good.unique.good.filter.unique.precluster.pick.pds.wang.taxonomy used in the example above)