We are switching our workflows over to Greengenes2, and we are noticing something that seems weird to us. Normally, we filter out sequences from chloroplast and mitochondria after classifying our reads using the following command:
qiime taxa filter-table
However, after classifying reads using Greengenes2, this does not filter any sequences. I suppose it's possible that no sequences are being classified as mitochondria or chloroplast, but this seems odd for our samples (primate feces). Should we be using other terms to exclude mitochondrial and chloroplast sequences? Or is this something we no longer need to worry about with the switch to Greengenes2?