I’m wanting to remove a list of OTUs from my data as they are likely contamainants. From the wiki, I understand the remove.otus command can be used to remove OTUs associated with a group, but not remove a specified OTU from all groups. Is that correct? If so, is there another command/or work around that can be used to remove specific OTUs?
I think you are looking for this, http://www.mothur.org/wiki/Remove.otulabels. You create an accnos file with the list of OTUs you want to remove. Something like:
Mothur will remove these OTUs from your files.
That worked great. Thanks.