Filter feature table based on taxonomy

[lautaro.rostoll]

Hello everyone!
After running DADA2, I filtered out my rep-seq based on sequence length, to remove any sequences that were too short.
I used the following command based on this post: Filtering out ASVs from DADA2 based on length - #4 by thermokarst.
qiime feature-table filter-seqs
–i-data trim-rep-seqs.qza
–m-metadata-file trim-rep-seqs.qza
–p-where ‘length(sequence) > 400’
–o-filtered-data filtered-seqs1.qza
After that, I did taxonomical classification using an amplicon-specific classifier using sklearn.
When I tried to do a taxa barplot I have the problem that there are some feature IDs that are not present in the taxonomy.qza file because I removed some sequences from the rep-seq file when I filter by seq lenght, but those feature IDs are present in the feature table.

I tried filtering out those feature IDs using the following command, but it run for several hours and the it crashed.
qiime taxa filter-table
–i-table trim-table.qza
–i-taxonomy taxonomy1.qza
–p-mode exact
–p-exclude "df328ed9e23e9e a802c48e3fc0fa68e1; 49b4951c905212d8a671647a253681d9; 9608adcdb80fe95c904395 c465537e3b; 942b345986d54917d3b13e6be81cf14a; a6d491a6a84ce2619169cd3538c63e 62; dff45ac694b2ef7186c0093a633fe5de; 44c4a170630b3d3ecebd657ccd8025c1; 65 fa2f461d4ba68b33bf45cb391e5e47; f3c4ba9a574064e92e84e4c6bd9f6d85; 18dc779e01 4ddff6a1930b6f0fc36844; a08dee45da8bf236f75aaa29b5d9d981; d29d4f22de8703dd09 351691a88b8ae6; b25c25dd8c4ea66d515ba4726a770f81; f2721c9022b3d0000ad4b9205a c91ccf; a426de20831b91b128502328779c0861; 48fd17f893369fea4a59608a90c5b4a4; cac5f1d3af38646bd58ec32c7570239a; 80dc1e882c31eb054a283adcc32c66ef; 606d46 f710fe184c2e74891b7d9177d7; 044485901c8eef72882ca8b965887bc1; 68f65eb31bbaf9 f92d61ba378a8d12b8; 62b9df9ec9666c59c505c8887183efc3; c299c4838a6d9720aa5b4e 7c40533b91; f98ba37b882428fa2a8cb47c6ab46e36; 09a65ef6f12541d910fed421f2a5b9 5b; 090078decff21ae8a4331fc1f9ec86d7; 468ffa2047e3544cd216b8c4f878723e; 00 f2449b8351431d61eb3e4bd6523da4; ca7cba37ae4d1d37d3c7f8bf17e9bd97”
–o-filtered-table trim-table1.qza

I would like to know if there is an option in qiime2 to remove the feature IDs from the feature table that we lost from the rep-seq when I removed the shorter sequences.
@thermokarst @Nicholas_Bokulich
thanks a lot!

Lautaro

[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 constru…

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

-Mike