I’m starting with data that is imported into QIIME at the OTU-table level (importing a
.biom file). I was using the
qiime feature-table filter-features plugin to remove singleton features (
--p-min-samples 2) as well as removing elements of the OTU table with fewer than 10 reads (
--p-min-frequency 10). This resulted in a filtered feature table which I can use for taxonomic assignment and other analyses.
However, because my filtered feature-table now contains fewer features than I started with, the sequences that I started with that map to the original feature table now have more sequences than what remains in my filtered one (I dropped 346 features from my dataset). 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. I thought that running with
--verbose might do the trick but it didn’t print out any additional info.
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!