dada2 denoise-single to get the ASVs: rep-seqs_qza.
And then I annotated the seqs with the downloaded
qiime feature-classifier classify-sklearn \
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?
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.
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