Hi
I would like to find the OTUs that are shared between different treatment groups. I have used the “venn command”, but that can only be used for the shared file- and all the samples?? Let’s say I have three treatment groups, and I want to find the core OTUs from these groups. Can I use my design.file for example to split the groups and then find the core OTUs?
Thank you very much!
Kristin
Mothur does not have a way to use the design file to select treatments from the shared file. It’s a good suggestion. I will add it to our features docket.
If you want to compare treatments to find core OTUs:
mothur > merge.groups(shared=yourSharedFile, design=yourDesignFile) - use the merge.groups command to create the treatment groups
mothur > venn(shared=current) - create venn diagram
or
mothur > get.sharedseqs(shared=current) - http://www.mothur.org/wiki/Get.sharedseqs
If you want to look at a specific treatment:
mothur > get.groups(shared=yourSharedFile, accnos=FileContainingTreatmentsGroupNames)
or
mothur > get.groups(shared=yourSharedFile, groups=TreatmentsGroupNames)
mothur > venn(shared=current) - create venn diagram
or
mothur > get.sharedseqs(shared=current) - http://www.mothur.org/wiki/Get.sharedseqs
Oh this is what I was asking about recently too. I just didn’t express it as clearly!