Hello,
I am new to using MEGAN/MALT and would like to make sure I understand the workflow correctly for my needs. I would like to obtain the taxonomic classification for my samples, but do it fully through the command line. I have processed samples through malt-run and have the corresponding alignment and .rma files. To obtain a text file with taxonomy classification, do I simply run rma2info on the .rma files?
Also, if I were to take the blast outputs for these samples (from blastn, not malt-run) and feed them through blast2rma and rma2info, would that be equivalent to the above steps?
Finally, I have run malt on a few samples on a database without taxonomy info. Is it possible to retrieve the taxonomic classifications from the .rma files without building a new database with that info?
Thank you for your help