Filtering before or after taxonomic assignment


I'm sorry in advance for what is probably an easy question. I am trying to filter my data (post demux, post-DADA2). I can filter the DADA2 output using qiime feature-table filter-features but for some reason the output of that filtering, when I try running it through qiime feature-classifier classify-sklearn gives me the error message "Parameter "reads" received an argument of type FeatureTable[Frequency]. An argument of subtype FeatureData[Sequence] is required.

I am not sure how to filter after taxonomic assignment as the output is classification.qza and the input to qiime feature-table filter-features requires a table input.

Any advice would be greatly appreciated!


To assign taxonomy, instead of feature table you need to provide rep-seqs.qza file, since you need sequences itself, not it's counts.

For this purpose, you can use another plugin.
Here is an excellent tutorial that can help as well.

This topic was automatically closed 31 days after the last reply. New replies are no longer allowed.