When I want to annotate blastn files on the linux command line version of megan, do I have to convert to rma format first? And must I use -mdb megan-nucl-Feb2022.db when running the blast2rma command? This results in very few annotated results.
Yes, you need to use the MEGAN nucleotide mapping database. If you are getting very few assignments, then there is probably a mismatch between the database that you aligned against and the mapping file. The mapping file is for use with NCBI-nt.
Also, I have uploaded a new nucleotide-alignment mapping database here (just incase problems are due to the fact that the current mapping DB is over one year old):