Filtering FeatureData[Sequence] using metadata file

[Nicholas_Bokulich]

@Matilda_H-D

when you use the filter-table filter-features command, both the feature table and the representative sequences file will be filtered

No — filter-features will only remove those features from the feature table, not from the sequences file.

@Matilda_H-D

Looking at the feature-table filter-seqs documentation, it seems like maybe this could be achieved using this command and passing in the same metadata file (i.e. list of features, not of actual sequences, to exclude) that would be used in filter-features? Is that right?

Correct. The process of generating a list of features that you can pass as metadata is mentioned further down in the same thread. The features-to-filter.tsv file described in that thread (the same list of features to filter from the feature table) would be passed to filter-seqs to remove those same features (sequences) from the FeatureData[Sequence] artifact that you have using the following command:

qiime feature-table filter-seqs \
    --i-data rep_seqs.qza \
    --m-metadata-file features-to-filter.tsv \
    --o-filtered-data control_seqs.qza

Generating that features-to-filter.tsv is described in this post (and in the future we may support a more direct method for generating such a file that contains features found in a single sample or collection of samples; I have raised an issue here to track progress)

Please let me know if that answers your question!