hi all;
is there a function that acts like a count table for OTUs? I know theres the relabund, but I’d prefer hard counts so I can cut out any low-representative samples.
Mothur has the remove.rare command, http://www.mothur.org/wiki/Remove.rare. You can run it with a shared file to remove OTUs with low abundance. This can be done with a cutoff byGroup or for the OTU as a whole. You might also like the split.abund command, http://www.mothur.org/wiki/Split.abund or filter.shared, http://www.mothur.org/wiki/Filter.shared.