I have been trying to use the new filtering features found in qiime2-2017.10. I want to remove any feature that is found in my control samples from all of my other samples. I read this post Mock Sample and PCR Blanks and was curious if the new qiime2-2017.10 update allows you to do this in one step? 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.
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.
@Nicholas_Bokulich thanks for the quick answer to my original question! At this time I do not see any better control to remove contaminant DNA that found its way in during extraction or PCR/library prep. The suggestion of analyzing the data set with the control sequences removed and present is an interesting idea. If anyone has any other control suggestions for the future that would be great!