Nice to meet you
While I study about microbiome analysis using qiime2, I have question at the step making phylogenetic tree.
After denoising step with DADA2 and Clustering, I got a table_clustered.qza file and representative_sequence_clustered.qza file.
Then, again, I modified table_clustered.qza file to remove singleton and non-bacterial OTUs. (final file name is table_clustered_singleton_non-bacterial.qza)
And I conducted making phylogenetic tree with representative_clustered.qza file without any modification.
Surely, that phylogenetic tree contains more amount of OTUs informations than modified table_clustered_singleton_non-bacterial.qza file.
Will that make trouble when I analyze beta-diversity (unifrac) with these two files?
If that is true, How can I reflect the table_clustered_singleton_non-bacterial.qza file OTU informations at representative_sequence.qza file.
Sincerely, I need your help.