Filtering Features found in Controls

[Nicholas_Bokulich]

Hi @Stream_biofilm,

@Stream_biofilm

Is the easiest way still to separate all features found in my controls, then create a metadata file with those features, finally use that metadata file to remove these features from the feature table?

Yes, that is one route for doing this. The other would be to use taxa-based filtering if there's a short list of taxa that you'd like to exclude. For filtering all features found in a specific sample, generating a list of features as a metadata file is still what you need to do.

@Stream_biofilm

I want to remove any feature that is found in my control samples from all of my other samples.

That might not be advisable, as many features (particularly if they are abundant) could represent cross-contamination from real samples; check out the notes in this thread.

I hope that helps!