Using taxonamy asigned to ASVs prior to vsearch clustering

Hi there,

I have used qiime feature-classifier classify-sklearn to classify my reads with the pre trained classifier silvia-138-99-classifier-nb.qza found here (I used pre-trained as I had some problem training my own classifier similar to those discussed here.

I am assigning taxonomy to my ASVs after merging all 18 batches. However due to some issue with a lack of shared features across samples, discussed here, I have later clustered my ASVs at 100 and 99%. Is it possible to use this previous taxonamy.qza on the later clustered feature tables?

I ask as feature names are all done by hashes of the sequences so i assume after clustering those hashes might change, or are just the centroid features kept and thus those hashes will still match those in the taxonamy.qza?

Hi @Lamm-a,

Yep. This should be the case. However, this can cause problems because you may end up using a very specific taxonomy to represent a cluster of sequences which may vary at the family and genus level. If you'd like to take into account the potentially varying taxonomy of sequences within a cluster, try using some of the RESCRIPt functionality to cluster your sequences and adjust the taxonomy accordingly.

For example try using the command: qiime rescript dereplicate ... Specifically, read through the help text on --p-mode, where you get to decide how to adjust the taxonomy for the resulting representative sequences of a cluster as defined by --p-perc-identity.


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