Hi every one,
I used QIIME 2 (201907) for taxonomic classification. I experienced a problem with classification of my archaea targeted 16s rRNA sequences with the plugin feature-classifier classify-sklearn. All the representative reads generated by Vsearch were classified as bacteria while taxonomic classification of the representative reads generated by Deblur seemed normal.
So, I tested Sklearn-classifier with 15 archaea 16s rRNA represent reads from Vsearch representative reads. The result showed something wrong that all the 15 reads were classified as bacteria.
when I remove one read, the result seemed normal.
Here are my command lines:
qiime feature-classifier extract-reads
qiime feature-classifier fit-classifier-naive-bayes
qiime feature-classifier classify-sklearn
How did the representative reads influence the taxonomic classification?