filtering feature table based on representative sequences

[anna-schrecengost]

Hi! I am utilizing qiime quality-control exclude-seqs to filter my denoised representative-sequences.qza file to only include sequences that are similar enough to my reference alignment. I would like to filter my feature table to only include these seqeunces as well. I don't see an option in exlude-seqs to accomplish this, or in qiime feature-table filter-features. Any help is appreciated, thanks!

[SoilRotifer (Mike Robeson)]

HI @anna-schrecengost,

The post linked below is a good example of how you can filter your feature-table based on your sequences. That is, your sequence file is the metadata file.

Rep-seqs length

Correct. You can follow the same approach used to remove chimeric sequences as outlined here. For example, if you want to keep the features in your feature table based on your sequence length criteria, you can just feed in your representative sequence file as a metadata file like so: qiime feature-table filter-features \ --i-table feature-table.qza \ --m-metadata-file sequences-to-retain.qza \ --o-filtered-table feature-table-retained.qza

You can also toggle the --p-exclude-ids / --p-no-exclude-ids option.

-Mike

[anna-schrecengost]

Thank you @SoilRotifer!