I followed the qiime2 commands to taxonomically affiliate seqs of marker gene (dsrB, herein) and finally obtained the phylogenetic composition via taxonomy barplots as shown below.
Q1: how do i know which features are included in a taxon, for example within the majority unidentified bacteria; ; ; ; ; ...
Q2: could i see a phylogeny used for this classification?
You can find such information in the taxonomy.qza file. One way is to visualize it as a .qzv file and open it in the browser or you can export it as a .tsv file and check it there.
For the phylogeny, I think, you will need to manipulate it outside of the qiime2 (or I didn't catch your question).
There is no phylogeny associated with taxonomy assignment. Quite often phylogeny and taxonomy do not match one other. If you'd like to make a phylogeny please see the Phylogenetic inference tutorial.
Thanks both of you for kind replies,
Hope that qiime develop a plugin to make a beautiful phylogenetic tree in future.
It may not be the best looking tree, but it's information dense, available in qiime2 right now, and comes with a great tutorial!
Example EMPress plot
thanks Colin, i will take look at it. HS
@baehsung, checkout out our latest phylogenetics video, by yours truly. The later part of the video (at ~9 minutes and 22 seconds) provides a simple example on how to use empress.
I am using empress to output my beta-diversity plot. You can search the position in the plot of the ASVs you are interested in by ASV ID.
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