Guidance for feature filtering step of qiime2

[colinbrislawn (Colin J Brislawn)]

@Qiime2_user

clearer guidelines on how to perform this step

That's fair, and it's not discussed in the gut-to-soil tutorial.

It looks like the pd-mice tutorial uses this command as a pre-filter before Differential Abundance testing. Here's the best info I could find:

@jwdebelius

I was involved in writing the PD mice tutorial and, to be honest, I can't remember the exact logic behind that specific depth. (I double checked my notes from that period, and... its not recorded :/. Sometimes that's the way it goes in this field: you pick a something and work with it). The mean/total abundance and prevalence co-vary pretty closely so most of the low abundance features will be picked up in your first filtering.

Zooming out a little bit, Qiime2 provides good default settings, so if there was a single 'right' way to do this, we would tell you.

This is a tradeoff between keeping rare features and removing noise, and that depends on the sources of noise for your sample and the biological signal you are trying to identify.

Also, I have found that reviewer three will not like my choice of --p-min-frequency, so later I'll have to change it anyway.