Behavior of rma2info

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?


hellow you could make a database only have bacteria/archaea

Unfortunately, as you probably suspected, the --bacteriaOnly flag only effects the taxonomic summary, functional counts still reflect all reads (and not just those assigned to bacteria).

The only way to get what you want is to use the extract to new document MEGAN feature, applied to bacterial nodes in the taxonomy viewer.

Indeed that was the behavior I saw, thanks for the reply!