Hi, I generated a .biom file using mothur SOP using a SILVA database. When loaded into MEGAN, it is automatically compared with the NCBI database, so the visualized data do not correspond to the taxonomy generated by SILVA - some taxons specified in OTU table are missing and some are probably assigned differently. In Megan Edit> Preferences> Use Alternative Taxonomy is grayed out. How to deal with it? Do I need to generate a different file than .biom from mothur? Why it is not possible to use alternative taxonomy with biom file?
Use Alternative Taxonomy is grayed out as soon as you do start any analysis in MEGAN. Restart the program and then first select the Alternative Taxonomy item before doing anything else.
Thank you for your reply Daniel, that works but what file should I choose as a different taxonomy to vizualize SILVA taxonomy not NCBI? I tried SSURef_132_Nr99_tax_silva_to_NCBI_synonyms.map, but this works when importing alignments I gues - it did nothing when my biom file was imported after that (if it’s supposed to work that I first set up a different taxonomy and then load the biom file). Some taxons are still missing in MEGAN vizualization like Intestinimonas and Monoglobus genus that I see in my BIOM file.
You need to download these files from the SILVA website: