Filtering sequences by feature table

[Nicholas_Bokulich]

@devonorourke

What I’d like to figure out is whether or not there is a trick in QIIME to pull down a list of the features that were dropped, so that I can then use that list to remove them from the sequences file too.

Filtering sequences based on a table is easy peasy, but I suppose you need to be a QIIME 2 dev to know its secrets.

filter-seqs has an optional table input. If you input a table instead of metadata, it will filter the sequences to only contain those found in the table.

@devonorourke

In any event, it would be a neat option to have within the filter-features argument set to retain the list of dropped features for exactly this purpose. Or maybe it already exists and I’m just missing it!

I agree, that could also be useful, but only in some cases. It is not super convenient, but you can always just re-run filter-features with the --p-exclude-ids parameter instead of --p-no-exclude-ids , or vice versa.

I hope that helps!