I noticed that my taxonomy.qzv and taxa-bar-plots.qzv have some descrepancies on the phylum level and I'm wondering where I went wrong.
This is my code to generate the two files:
# Assign taxonomic information to the ASV sequences
qiime feature-classifier classify-sklearn \
--i-classifier taxonomy_assignment/silva-138-99-nb-classifier.qza \
--i-reads quality-filtering/rep-seqs.qza \
# Genearte human-readable summary of the taxonomic annotations
qiime metadata tabulate \
--m-input-file taxonomy_assignment/taxonomy.qza \
qiime taxa barplot \
--i-table quality-filtering/table.qza \
--i-taxonomy taxonomy_assignment/taxonomy.qza \
--m-metadata-file sample-metadata.tsv \
When I look at taxa-bar-plots.qzv, I see that verrucomicrobiota has a much higher frequency than proteobacteria. However, when I look at the taxonomy.qzv it looks super wrong (only one instance of verrucomicrobiota).
On R, I made a phyloseq object (physeq) with the following feature table and taxonomy.qza. I have also attached the output of:
This is data that has already been analyzed and I'm using it to practice. The results from the previous analysis done by our bioinformatician shows that Verrucomicrobiota should be much more prevalent.
Thank you for all your help!