OTU calling

It would be very useful to be able to incorporate data from classifier programs such as the RDP classifier. For example, instead of referring to an OTU by its index or the name of a representative sequence, it would be useful to be able to display the taxonomic unit to which it corresponds (as determined by a classifier).

I suppose this would require something like a “taxon_names” file, with the sequence ID in one column and taxonomic information in the remaining columns, and then have the option of looking up and using taxonomic info in the various summary() commands.

Does this make sense? Is it already possible?

Yeah, it makes sense. So you can already do the get.oturep command, which will give you the representative sequence from each OTU. For the time being you can take that fasta file and upload it to the RDP. We’re currently developing a classifier that allows you to try different methods and taxonomies. Hopefully, this will be done by the end of the year.

cool. In the meantime I can hack it with scripts. Thanks, Pat.