I am checking only antimicrobial resistance genes from genomic/metagenomic reads and contigs, and not all but many proteins or nucleotides turned out “no hit” or “not assigned” on SEED or other functional analyses. My objective is to prepare a matrix of many samples/sources using the comparison of Megan.
Is there any way to modify the mapping file to make “no hit” and “not assigned” to be assigned, and/or to customize the functional/taxonomy analysis for a certain database?
If you want to map additional reads to taxonomic or functional classes, then you can setup a “synonyms” file that contains a word that appears in the header of the reference sequence that corresponds to the class and the id of the class. Use the Set Synonyms File menu item or meganizer command-line option to use that file in additional to the other mapping files and that will also be used to recruit reads to classes.
(Does that answer your question, I am not certain that I understood you correctly)