Retain all ASVs collapsing to specific genera

[pau]

Dear community, I need help with the following:

I have a feature table (ASVs) that collapses into more than 1,000 genera. However, I am interested only in a core-group of about 70 genera.

My question is: is there a way to filter my ASV table to retain only those ASVs that collapse into the 70 genera of interest?

I don't know if I explained properly...

Thanks in advance!!

[timanix (Timur Yergaliyev)]

Hello!
Please, check filtering tutorial, especially taxonomy based part of it, and this post. You can find right commands in the tutorial and examples in the post.

[pau]

Hi @timanix , thanks for your quick answer!

I am trying to build my command, something similar to this

qiime taxa filter-table
--i-table table-1.qza
--i-taxonomy TAXA/taxonomy-1.qza
--p-include g__Moraxella,g__Oscillospira,g__Prevotella
--o-filtered-table filtered_all_taxa_to_keep.qza

It worked when I only added classified genera. However, I am having problems when I have to add unclassified genera (classified to family or order), such as these:

• k__Bacteria;p__Bacteroidetes;c__Bacteroidia;o__Bacteroidales;f__S24-7;g__
• k__Bacteria;p__Bacteroidetes;c__Bacteroidia;o__Bacteroidales;f__;g__

How should I write them? I've tried different things but with no good results!

[timanix (Timur Yergaliyev)]

Did you try something like this?

"o__Bacteroidales;f__S24-7"

[pau]

Yes, I did. And this doesn't select anything.

when I try this group alone the error apearing confirms that.

qiime taxa filter-table
--i-table table-1.qza
--i-taxonomy TAXA/taxonomy-1.qza
--p-include "o__Bacteroidales;f__S24-7"
--o-filtered-table filtered_all_taxa_to_keep.qza

Plugin error from taxa:

All features were filtered, resulting in an empty table.

I don't know what can be happening!

[timanix (Timur Yergaliyev)]

@pau

I don't know what can be happening!

I am not sure as well.
But there is a workaround:

Option 1. Visualize taxonomy file (as qzv) or export/extract a tsv file stored in taxonomy.qza. Get a list of ASV, assigned to desired taxa and use that list to filter the table.

Option 2. Export taxonomy as a tsv table, add substring to desired taxa, for example, "keep_me" at the end. Import it back as taxa_to_keep.qza. Use added substring and taxa_to_keep.qza to filter the table. In further analysis just use your original taxonomy.qza file.

[pau]

Hi @timanix !
I realized that these features need to be written with a space between in order to be selected ("o__Bacteroidales; f__S24-7; g__;")

I was able to extract the desired ASVs from taxonomy.tsv.

Thanks a lot for your time