Finding cores

How do I find the otus and their representative sequences that are shared by ALL groups in a groups file?

I thought I knew, but can’t seem to make anything work. I keep recovering all the OTU representatives from all the groups.

The problem is to locate the “core microbiomes”, the set of OTUs shared by all people in a given microbiome.

So here’s what I would suggest:

First the get.sharedseqs command, by default it will select the otus unique to ALL the groups in your groupfile.

get.sharedseqs(list=abrecovery.fn.list, group=abrecovery.groups, output=accnos, label=0.10)

Then the get.seqs command to select these sequences from the files you need as inputs for get.outrep

get.seqs(accnos=abrecovery.fn.0.10unique.C-A-B.accnos, fasta=abrecovery.align, list=abrecovery.fn.list, group=abrecovery.groups)

Then get.oturep, but make sure the label is the same as the get.sharedseqs. Mothur would output the other labels but their shared otus are different.

get.oturep(fasta=abrecovery.pick.align, list=abrecovery.fn.pick.list, group=abrecovery.pick.groups, phylip=abrecovery.phylip.dist, label=0.10)

I hope this helps!