I am having an issue understanding some discrepancies using
qiime feature-table core-features. When I run core features on a feature table that hasn’t been combined with taxonomy yet, the number of core features is much different than if I were to run the script on a feature table that has been combined with taxonomy at the species level. When I try it with a feature table at the phylum level, it is also very different than the other two. Why are the number of features and core features changing depending on whether my feature table has been combined with taxonomy or not?
I’m attaching the qzv files in case that helps.
Here is the core feature without taxonomy core-otus.qzv (255.7 KB), with taxonomy at species level infectedcorefeatires.qzv (235.1 KB), and with taxonomy at phylum level core-phyla.qzv (235.7 KB).