Hi,
I have one set of same patients with two sequencing files - 16S files and shotgun files, I am trying to compare their results using greengenes2. I use woltka for wgs data to get OGU table and use the following command to get 16S greengenes2 OTU table:
qiime vsearch cluster-features-closed-reference \
--i-table feature-table.qza
--i-sequences rep-seqs.qza
--i-reference-sequences 2024.09.seqs.fna.qza
--p-perc-identity 0.97
--o-clustered-table clustered-feature-table.qza
--o-clustered-sequences rep-seqs-clustered.qza
--o-unmatched-sequences unmatched-seqs.qza
Next I use their combined feature id to subset the reference phylogenetic tree and try to annotate the tree, It seems that the subset tree has a misgroup problem and some features of 16S look not correct. Do you have any thoughts? I attached part of my tree here, orange represents 16s and blue represents WGS.
