qiime taxa filter-table for 'D_0__Bacteria'

Hello, Using qiime2-2019.1 I ran command below to filter taxonomy results to only include ‘D_0__Bacteria’ However, the results included all Bacteria, whereas I only want to the kingdom bacteria level.

qiime taxa filter-table
–i-table /qiime2Files/table.qza
–i-taxonomy /qiime2Files/rep-seqs.qza
–p-mode exact
–p-include ‘D_0__Bacteria’
–o-filtered-table /qiime2Files/bacteria-level.qza

I also tried to use the --p-mode exact parameter to ensure only those taxa at the bacteria level were included in the output file and no additional taxon levels were included.

I believe my syntax is incorrect.

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Hi @microbiomeAnalyst,
I don’t know exactly what your data looks like, so please forgive me if I’m way off base here. It looks as though your command is include-ing all features in Domain Bacteria (D_0), when what you’re really looking to include is Kingdom bacteria (K_1, maybe).

Am I barking up the wrong :palm_tree: here?

@microbiomeAnalyst, I’d like to retract my suggestion above, and ask for clarification about your question. I’ve spent a lot of time with GreenGenes taxon strings lately, and in that context D_0 seemed like a reasonable prefix for Domain.

Can you clarify what you mean here?

Are you trying to filter non-bacterial features out of your table? Are you trying to group all of your features together at the kingdom level? (which you could do with qiime taxa collapse) Is it something else you’re going for here?


Hello Chris. Thank you for your assistance. I am trying to filter for D_0_Bacteria only so that I can command BLAST these and understand what type of taxa they are cumulatively. So I am trying to get a filtered list of only those features which match ‘D_0_bacteria’

Please excuse me for misunderstanding - what results are you getting that don’t match ‘D_0_bacteria’?

Hey @microbiomeAnalyst, are you trying to filter for features that don’t have taxonomic resolution beyond the Kingdom level?

If so, you could use use --p-exclude to filter out features with D_0__Bacteria;D_1__.
Let me now if that’s not what you’re going for.

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