I am fairly new to qiime2 (and microbiome analysis in general) and have gone through the moving picture tutorial without much trouble, however I have a few questions regarding the use of the feature table for diversity measures compared to using the collapsed tables (by taxonomy).
It makes more sense to me to merge together all features with the same taxonomic assignation (collapse) and then calculate the diversity metrics on those tables.
For instance I like the heatmaps we can get, and those make sense to me:
In this idea I went to calculate some simple alpha and beta diversity metrics on the feature tables collapsed at the genus level. Is this something “legal” or does it make absolutely no sense ?
In the case it makes some sense, how can I calculate diversity metrics that needs a phylogenetic tree such as the UniFrac distances ?