I have been using
rma2info to summarize information from metagenomics RMA files. It works great! However, I am now working with an RMA file produced from an insect sample. The main focus was to assemble the insect genome, but a secondary use is to find all bacteria present. When using
rma2info for this RMA file, there are plenty of non-bacteria assignments (which is expected). However, I’d like to summarize only taxonomic and functional class counts for the bacteria/archaea present. I saw that there is a
--bacteriaOnly flag, which will restrict this for the taxonomic report. My question is, will the
--bacteriaOnly flag also restrict this for the functional class counts?