Hi, so I am dealing with a collaborator that doesn’t want to give me all the files used in generating the OTUs for our project. I would like to extract sequences for specific samples from the fasta file he has sent me, and in the example on the get.groups command page it indicates that in order to do this I need a groups file (or, that is the file type used in the example).
Is it possible to use the fasta option in get.groups with a list or a shared file? My collaborator tells me these should be good enough for what I want to do, though I think it likely that he doesn’t understand what I want to do. My goal is to extract the nice clean trimmed mothur sequences I want and map them to sequences from another file entirely using usearch.
Thanks for any advice,