Filter table : taxonomy

Technical Support
1

Hi all,
I am trying to filter my taxonomy table by removing specific entries (Chloroplast, Mitochondria, Eukaryota ..), but in the final table only the Chloroplast sequences were actually removed. I execute the command below:

qiime taxa filter-table 
--i-table table-filtered.qza 
--i-taxonomy taxonomy.qza 
--p-exclude Chloroplast,Unassigned,d__Eukaryota,
d__Bacteria; p__Proteobacteria; c__Alphaproteobacteria; o__Rickettsiales; f__Mitochondria; g__Mitochondria; s__,
--o-filtered-table final-table.qza

In the forum, I found that by default no taxa are excluded, is there any specific delimiter character ? Thank you

--p-exclude TEXT One or more search terms that indicate which taxa
should be excluded from the resulting table. If
providing more than one term, terms should be
delimited by the query-delimiter character. By
default, no taxa will be excluded.

2

Hi @Zeina,

You could do a condensed version like:

--p-exclude Chloroplast,Unassigned,d__Eukaryota,f__Mitochondria;

If you want to remove an entire taxonomy string, you should be able to put qoutes around the string that contains spaces, e.g. "d__Bacteria; p__Proteobacteria;..."

-Mike

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