.extraction and .taxonomy files


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!

What is an “extraction” file? I’m pretty sure it isn’t being created by mothur.

Yes, sorry, the extraction file was coming from Metaxa, which is why it was different. Thanks for bringing that to my attention!