I am using fragment-insertion plugin in qiime2 and I am not quite clear about the insetion-tree.qza. Could you please help me to understand more about this? I also read the paper but couldn’t find answer to the question that I have.
My question is as follows.
I have 7000 unique ASV and I run following command to make the tree by using fragment-insertion plugin.
qiime fragment-insertion sepp
After running the script, I uploaded insertion-tree.qza in iTOL (interactive Tree of Life) and I noticed only 193 branches.
My first question: Why are there only 193 branches for 7000 unique ASV? Why not 7000?
My second question: I checked the branches names assigned in the insertion-tree.qza and I tried to annotate with the taxonomy_gg99.qza (https://raw.githubusercontent.com/biocore/q2-fragment-insertion/master/taxonomy_gg99.qza) and most of the branches are annotated with Archaea. I took the branch id name from insertion-tree.qza and directly annotated with same id available in taxonomy_gg99.qza.
Could you please help me understand what is going on? Am I missing something?
Thank you so much.