Filter feature table based on taxonomy

[SoilRotifer (Mike Robeson)]

If I understand correctly you want to keep only the features in trim-table.qza that are present in your filtered-seqs1.qza, and remove the rest. If so you can do the following:

qiime feature-table filter-features \
    --i-table ./trim-table.qza \
    --m-metadata-file ./filtered-seqs1.qza \
    --o-filtered-table ./trim-table1.qza

You can apply --p-exclude-ids if you want to remove the IDs present in --m-metadata-file. The default is to keep the IDs.

Also you can use RESCRIPt to filter the taxonomy files and the sequences by length too. Check out the tutorial here:

Processing, filtering, and evaluating the SILVA database (and other reference sequence data) with RESCRIPt

Please consider this tutorial a living document, which may change based upon community feedback and ongoing plugin development. RESCRIPt RESCRIPt (REference Sequence annotation and CuRatIon Pipeline) is a python package and QIIME 2 plugin for formatting, managing, and manipulating sequence reference databases. This package was designed for compiling, manipulating, and evaluating sequence reference databases from SILVA, NCBI, Greengenes, GTDB, and other sources, and for construc…

Check out qiime rescript filter-taxa ... (I do not think it made it into the linked tutorial).

-Mike