I used MOTHUR to get taxonomic information from silva, and discovered that the reads present in my .extraction file (and given a potential general classification, e.g. Bacteria) do not match up to the reads present in the .taxonomy files; there are reads in the .extraction file that do not show up in the .taxonomy files. Do the general taxa categories in the .extraction file originate from a different reference database? Why else might this be happening?
I’d appreciate any input!