My issue is similar to 2525. I have AMF amplicon. Following Nicholas_Bokulich suggestion in this issue, I am using a two-step approach, which consists:
- Classifying my repseqs.qza using MaarjAM through classify-consensus-blast
- Classify the Unassigned sequences using classify-sklearn using SILVA 132 18S dataset.
I have all set and was able to import MaarjAM sequences and classify using blast, using the following command:
qiime feature-classifier classify-consensus-blast --i-reference-reads maarjAM_seq.qza --i-reference-taxonomy maarjAM_taxonomy.qza --p-perc-identity 0.99 --i-query 2-dada2_repseqs.qza’ --o-classification 3-consensus-blast.qza
Next, I generated taxa barplot and confirmed the existence of several unassigned.
The problem is that I cannot figure out the next step, do I have to filter Unassigned ASVs from 3-consensus-blast.qza ? Can I do this using filter-seqs ?
After that do I have to merge objects generated with classify-consensus-blast and classify-sklearn into one?