Error message with qiime feature-table filter-seqs

HI Everyone,

I’m trying to use the feature-table filter-seqs function, added in qiime2-2017.9.

I’m using this command below:

qiime feature-table filter-seqs
–i-data table-S4.qza
–m-metadata-file Sequences-to-remove_from_S4.tsv
–p-exclude-ids
–o-filtered-data table-S4-filtered.qza

In the metadata file, I have only the PCR blank (using as header, Index). I’m trying to remove all sequences found in this blank from the other samples. I’m getting the following error message:

Plugin error from feature-table:

Argument to parameter ‘data’ is not a subtype of
FeatureData[Sequence].

Interestingly, replacing table.qza for rep-seqs.qza in the same command, it completes with no error message.

qiime feature-table filter-seqs
–i-data rep-seqs-S4.qza
–m-metadata-file Sequences-to-remove_from_S4.tsv
–p-exclude-ids
–o-filtered-data rep-seqs-S4-filtered.qza

Am I doing something wrong? Using the feature-table filter-seqs, is it possible to remove the sequences also from the table.qza?

Thanks in advance,
FS

Hey @fstudart,

qiime feature-table filter-seqs is only for FeatureData[Sequence].

To filter FeatureTable[Frequency] you can use qiime feature-table filter-features in exactly the same way as your filter-seqs call above. That will remove all of the features IDs listed Sequences-to-remove_from_S4.tsv for every sample.

Let me know if that doesn’t accomplish what you need!

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