Following this discussion: Qiime taxa filter-table filtering multiple taxa
I was wondering if I can filter out multiple taxonomy strings simultaneously.
Here's my goal:
I have about 20 taxa identified in my negative control. Some of them were at family level, some of them went all the way to the species. I want to to remove these exact 20 taxa in my other groups before running diversity tests.
I was able to filter them individually using following command:
qiime taxa filter-table
--p-exclude "d__Bacteria; p__Proteobacteria; c__Gammaproteobacteria; o__Pseudomonadales; f__Pseudomonadaceae; g__Pseudomonas"
However, I don't know how to filter multiple annotations at the same time. I tried to put a comma in between ("...","...") but only the first one got filtered. Is there a way to do that? I hope I don't have to repeat the same command 20 times.
In addition, I am looking to removing these taxa proportionally, using modules such as FEAST or SourceTracker2.
My understanding is that FEAST is still under development if I want to use it as a QIIME2 plugin. Is that correct?
I found this tutorial for SourceTracker2 (https://github.com/biota/sourcetracker2/blob/master/ipynb/Sourcetracking-using-QIIME2.ipynb). Is there an official tutorial on the Qiime2 website?