classifier question

does “silva-132-99-515-806-nb-classifier.qza” classifier contains bacterial and archaeal16S, as well as 18S data, or just bacterial 16S

Cause when I do classification with my 16S data, I can see all three domain in my taxonomy file

archaea, bacteria, Eukaryota

Thank you very much

silva-132-99 contains 16S + 18S sequences

silva-132-99-515-806-nb-classifier.qza contains all of those sequences that are amplified by the primers 515f + 806r

whether that includes eukaryota I am not sure, but your results seem to suggest that is the case.

if I want to training both 16S and 18S together by using silva_132_qiime_release

do you know which two (sequence and taxonomy) files are good for this in QIIME2

Thank you very much

Use the full-length SILVA pre-trained classifier that does not have 515-806 reads extracted. If you want to train your own, use the SILVA full-length 16S+18S reference sequences clustered at 99% OTUs.