Best way to get taxonomy report/data for a single group?

I’ve run through the MiSEQ protocol for a number of samples. The PI I’ve done the work for actually wants a very simple sort of report - a list of the OTUs present in each group along with the taxonomic classification and the prevalence count (actually they don’t care about the OTU so much as just the taxonomic classification/species and prevalence).

What’s the best way to do this in a group-wise fashion, e.g. one group at a time?


If I clearly understand what you need.
You can run the classify.otu() command with the list file, the count file, the taxonomy file and basis=sequences.
example: classify.otu(list=file.list, count=files.count_table, taxonomy=files.taxonomy, label=0.03, basis=sequence)
You will have an output ending by that give you the table you are looking for.

Hope that help,


And that worked brilliantly. For some reason I never thought that classify.otu would generate that matrix, and I’d never actually looked at the *.tax.summary file! I owe you a beer. :slight_smile: