Filter taxa seqs and table

I have tried to filter seqs and taxa table using the following commands providing the taxa IDs I want to exclude:

qiime taxa filter-seqs --i-sequences Analyses/all_rep-seqs-nonchimeric.qza --i-taxonomy Analyses/all_taxonomy-nonchimeric.qza --p-exclude 36c022004ac46f0a73a46fd4830d708e,887de3e2e9019d6ae15b1a2bf059bac5,60901fc0849dc9fb75de6b5c0267fab4,af1bb615e0ac8b9e2b52512dd76d34b0,4f76be318b9b940183a73680b452598f --p-mode exact --o-filtered-sequences Analyses/all_filtered_rep-seqs_nonchimeric-nocontaminants.qza

qiime taxa filter-table --i-table Analyses/all_table-nonchimeric.qza --i-taxonomy Analyses/all_taxonomy-nonchimeric.qza --p-exclude 36c022004ac46f0a73a46fd4830d708e,887de3e2e9019d6ae15b1a2bf059bac5,60901fc0849dc9fb75de6b5c0267fab4,af1bb615e0ac8b9e2b52512dd76d34b0,4f76be318b9b940183a73680b452598f --p-mode exact --o-filtered-table Analyses/all_filtered_table-nonchimeric-nocontaminants.qza

However, when I view the resulting files, they still have the taxa IDs I wanted to remove. Am I doing something wrong?

Hi @Jewelna_Osei-Poku,

It doesn’t seem like it should be the right solution, but have you tried passing in a file with the list of the names you want to exclude, one per line?

It also matters less for your taxonomy whether or not the sequence IDs are present (it matters much more in your table) because feature-based analyses should focus on what’s in your table verses whats in your taxonomy.

Best,
Justine

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I will agree with @jwdebelius
You can use

qiime feature-table filter-features \
    --i-table table.qza \
    --m-metadata-file ids_to_exclude.tsv \
    --p-exclude-ids \
    --o-filtered-table filtered-table.qza 

and provide a metadata that contains IDs to remove

Feature ID
36c022004ac46f0a73a46fd4830d708e
887de3e2e9019d6ae15b1a2bf059bac5
60901fc0849dc9fb75de6b5c0267fab4
af1bb615e0ac8b9e2b52512dd76d34b0
4f76be318b9b940183a73680b452598f

To filter table should be enough, no need for the analysis to filter rep-seqs file.

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Thanks @jwdebelius and @timanix. Your suggestions worked.

1 Like