get.oturep from get.sharedseqs?

Commands in mothur
1

Hi all -
So, <get.sharedseqs> outputs a *.shared.seqs file. This file lists ALL sequence names associate with a particular shared OTU. Is there a way of obtaining a list of representative shared OTU’s? In other words, if my groups share 11 OTU’s is it possible to get a representative list of those OTU’s - a list with 11 names? Basically a <get.oturep on a shared file. I have tried different approaches but with no success…

What I would like to do is run <classify.seqs> on the OTU’s shared between groups but I do not require the redundancy provided in the .shared.seqs file.

Thanks

jarrod

2

Did you ever figure this one out? I am struggling with the same thing at the moment.

3

You can use the classify.otu command to get the classifications for all the otus, and then use the get.sharedseqs to find what otus are shared by the groups you are interested in. Both the classify.otu and get.shared seqs list the otu number, unfortunately, you would have manually weed through the output file from classify.otu to find classifications you want.

4

Thanks. Are there any plans to add this as a feature to a future version of Mothur?