Only 2 two taxa from 18S taxa barplot

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Hi @Namraj_Jaishi,

Based on your taxonomy plot It appears that your sequences are in the reverse orientation. Which means taxonomy assignment will not work when using qiime feature-classifier fit-classifier-naive-bayes, as the sequences must match the orientation of the reference database. I recommend orienting your sequences using RESCRIPt as follows:

qiime rescript orient-seqs \
    --i-sequences  rep-seqs.qza \
    --p-threads 8 \
    --o-oriented-seqs   rep-seqs-orient.qza \
    --o-unmatched-seqs   rep-seqs-non-orient.qza

Then use the premade silva classifier on rep-seqs-orient.qza, and see what you get.

Alternatively, try using qiime feature-classifier classify-consensus-vsearch ... , as orientation of your sequences will not matter, and you should be able to obtain taxonomy.

Let us know if either works.

-Mike

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