Different annotations for seqs and its corresponding reverse seqs

I use dada2 denoise-single to get the ASVs: rep-seqs_qza.
And then I annotated the seqs with the downloaded silva-132-99-nb-classifier.qza

qiime feature-classifier classify-sklearn \
   --i-classifier silva-132-99-nb-classifier.qza
   --i-reads rep-seqs.qza

In my results, I found two seqs are the same, seqA and seqB.
seqB is the reverse complement of seqA.

However, I found the annotations reports which generated by qiime feature-classifier classify-sklearn
are complete different for them.

So, is there something wrong?


Hi @111,
Your sequence data are in mixed orientations.

As documented a few times on this forum, the classify-sklearn method specifically (but not other taxonomy classifiers) assumes that the data are in a single orientation.

Thus, you must orient your reads prior to classifying. Fortunately, we have a new plugin to achieve that, see the tutorial here:

Or use one of the other taxonomy classification methods in q2-feature-classifier.

Good luck!

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