Dear Mothur team,
I would like to export the OTU sequences generated in mothur and add them to a database-like structure, like SQL. I found get.outrep to be very helpful here. There was only one thing I could not figure out, when I do have groups: how can I assign the number of sequences per group in the -outfile. At the moment I skip the group&groups option and combine the output with a transposed version of the OTU.share file, which is a little cumbersome. I would be very greatful if there is another solution to this :).
Many thanks in advance,
Try the get.groups command
get.groups(group=mergegroupsgood, shared=All.good.filter.square.an.shared, groups=EF1-EF2-EF3-EF4-EF5-ESS-ESW-EKW-EKS-EES-EEW)
I found that you need to name every group you care about, even if the answer is all of them.
Output will be several shared files at each otu definition(or use the label=unique-0.01-0.03 command to only output the label or labels you care about), Open it in excel which will title each otu# the same as get.oturep and will list each group, and tell you number of seqs from each otu in each group.
Ive found that some =sum() and some conditional formatting in excel makes it much easier to read and make comparisons between groups.