Filtering before or after taxonomic assignment

[jaaronson]

Hi!

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!

[timanix (Timur Yergaliyev)]

Hello!

@jaaronson

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.

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

@jaaronson

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.

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