Difference in classification with complete sample set and a subsample

[Mudit_Bhatia]

Thank you Colin for the response.

I did the complete analysis of the run in subsets and got most of the subsets which resulted in fairly nice classification. I am trying to stick to Silva-138.1 classifier which is available on the qiime2 website as I have been having issues training the feature classifier by myself, something I am discussing here

I have tried using both Rescript protocol and the protocol for qiime2 versions before 2024.2. Is there any other way I can try

@colinvwood

This can happen either when the sequences to be classified are in mixed orientation or when there's a nonsense sequence among them that causes the orientation detector to assume the wrong direction. Do you know whether your sequencing pipeline would have resulted in mixed orientation reads? If so, use qiime rescript orient-seqs to orient them consistently. If not, I would try rerunning classify-sklearn once with the --p-read-orientation parameter set to 'same' and once with it set to 'reverse-complement' and then check those taxonomies.

without having to train the feature classifier?