I want to remove sequences that, when clustered into phylotypes, occur 99 times or fewer in a particular group(sample). Unfortunately, the remove.rare only works on a shared, list, rabund or sabund file. After I remove them from the shared file I’d like to then classify the phylotypes using classify.otu but that command only works on a list file. If I go back and remove the rare sequences from the list file, it can only remove sequences that occur 99 times across all groups since it does not have the bygroup option available. As a result, when I classify the phylotypes I find groups that have phylotypes which occur 99 or fewer times, which is not what I want.
Is there a way to have a group, name and taxonomy option included in the remove.rare so I can remove these sequences completely from all further analyses? Or is there another workaround? I don’t believe that phylotypes which occur less than 100 times in any sample can be trusted to I want to remove them from all further analysis.