Hello and thanks for this great community!
I am using qiime2 and r for my analysis.
After dublur I usually export the feature table and taxonomy to r, then for alpha and beta diversity I do rarefaction with phyloseq.
Usually, for differential abundance analysis, I use the raw biom table and collapse to genus level.
Today I was asked to generate a rarefied table at the genus level. If I’m doing rarefaction of the feature table and then collapsing to genus - I get very different row sums for each sample.
Is it possible that I am losing genera that were unclassified to the genus level?