Filtering multiple taxa with exact substrings

[Yangh191 (HY)]

Hi~

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
--i-table sam4_tab_f2uv3_01.qza
--i-taxonomy sam4_tax.qza
--p-mode exact
--p-exclude "d__Bacteria; p__Proteobacteria; c__Gammaproteobacteria; o__Pseudomonadales; f__Pseudomonadaceae; g__Pseudomonas"
--o-filtered-table f4_test.qza

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?

Thanks
Hui

[colinbrislawn (Colin J Brislawn)]

Hello Hui,

Welcome to the forums!

There is a way to filter multiple taxa at the same time, however I think there's a better way to think about taxa that appear in your negative control.

@Yangh191

I have about 20 taxa identified in my negative control. ...
I want to to remove these exact 20 taxa in my other groups before running diversity tests.

ah... that might cause other problems.

The Illumina platform suffers from index-hopping between samples, and the most abundant amplicons are the most likely to 'hop' into other samples because of a mismatched barcode. This means that a perfectly empty negative control would still get some reads assigned to it by the Illumina sequencer, and essentially be a tiny subset of all real amplicons. Because this happens during sequencing, real amplicons may end up in empty negative controls.

@Yangh191

In addition, I am looking to removing these taxa proportionally, using modules such as FEAST or SourceTracker2.

That's a much better idea! We have discussed some methods like this, and I think that's the way to go.

It looks like FEAST it still tagged as a beta, but you could still try and get support from the developer! You could also check out q2-quality-control or decontam, which have similar goals.