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:
remove.lineage(fasta=seqs.good.unique.pick.txt, count=seqs.good.pick.count_table, taxonomy=seqs.good.unique.pick.2019_taxonomy.wang.taxonomy, taxon=Fungi_unclassified-unclassified_Fungi)
Again, I’m probably just being dense about this, but I would love to figure this out.