How to determine the number of reads lost after filtering out unwanted ASVs from the FeatureData[Sequence] artifact (rep-sees.qza)

Hi, so I have a list of ASVs. I used that list as a metadata file to filter these ASVs to be retained using this script.

qiime feature-table filter-seqs
--i-data output/rep-seqs.qza
--m-metadata-file metadata.txt
--o-filtered-data output/pmoA_filtered.qza

Based on that, I used the rep-seqs artifact as the input file. Now, my question is, how do I know if I lost too much reads after filtering?

Hi @pkmnsandy,

You could complement it with qiime feature-table filter-features using the filtered sequences as your metadata. Then, you could check the depth of the new table.


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