I’m trying to determine which OTU’s are unique to specific conditions - sharedotus will tell me which OTUs they have in common, but if doing a Venn comparison of more than 2, determining the unique OTUs to a specific condition is a bit tricky. Any hints?
An update - I read in the docs that you could use groups to specific the groups in get.otus, so I tried:
get.otus(groups=TB_noIAI, shared=stability.tx.PTBIAI.shared, constaxonomy=stability.cons.taxonomy, accnos=stability.trim.contigs.good.unique.good.filter.unique.precluster.denovo.vsearch.accnos)
And mothur said:
groups is not a valid parameter.
Seems like this might be what I want, as it would get me the otus for just one group (or multiples) - I’m confused, is groups not working?
The get.sharedseqs command, https://mothur.org/wiki/Get.sharedseqs#uniquegroups_.26_sharedgroups, is a better fit for what you are looking to do.
To find the OTUs that contain only sequences from a set of groups (unique to), run the following:
mothur > get.sharedseqs(shared=yourSharedFile, uniquegroups=group1-group2, output=accnos) - list OTUs that are unique to group1/group2
To find all OTUs containing sequences from a set of groups (shared by), run the following:
mothur > get.sharedseqs(shared=yourSharedFile, sharedgroups=group1-group2, output=accnos) - list OTUs that are contain sequences from group1/group2