However, for the Parkinson mice tutorial, a filtering of samples, based on rarefaction depth, is conducted, before creating the taxa-barplot visualization.
My interpretation is that in the Parkinson mouse tutorial, they are looking to visualize as barplot the composition of the samples retained after the rarefaction step. One way to do this is to filter out any samples with less than your rarefaction threshold. Another way could have been to create a list of sample identifier from the file 'core-metrics-results/rarefied_table.qza' and providing this list as metadata for the 'feature-table filter-samples' plug in.
Performing the filtering by excluding the samples with less than threshold used in the rarefaction step, comes in handy so it becomes already the initial step for the de analysis for the tutorial, which it is always a good idea to perform after filtering out low count samples/ASVs.
So to answer your question, I would say it is a matter if you want to visualize the samples passing the rarefaction step as separate group or it is enough to visualize them in the context with the rest of the samples.
Ok, perfect! So it depends on what do you want to visualize, but going forward in your taxonomic analysis with all the samples. without filtering them, would also be correct, right?
