Filtering representative sequences


Is there a way to filter features from your representative sequence file based on a .tsv of indexes, as you would from a feature table? Or, alternatively, to extract representative sequences from a filtered feature table?

Thank you!

Hi @Lorinda,

Sorry for the very delayed response.

I’m afraid we don’t have a way to filter the representative sequences at this time. The feature-table also has no idea what the representative sequences are, it just has IDs and the associations between them. So it can’t really help here either.

Having extra sequences in your FeatureData[Sequences] artifact should’t generally be a problem downstream in QIIME 2, but I take it you are trying to use these outside of QIIME 2 for something else?

@ebolyen For example, if I wanted to assign taxonomy elsewhere, or submit filtered, representative sequences to a database somewhere. For now though, it seems like there is an easy enough work around through QIIME 1, using the filter_fasta command. Thanks!

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Just a note, I created an issue to track progress on this feature. We’ll follow up here when it’s available in a release (likely within the next 2-3 releases).

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We now support filtering FeatureData[Sequence] with feature-table filter-seqs in QIIME 2 2017.9!

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