I’m having some issues to obtain the plot score for my mock samples composition comparing observed against expected. The thing is that the qiime2 analysis (step assign taxonomy) are done against SILVA database who has this aspect when you get a taxa for a feature:
where 0 is domain, 1 is phylum, 2 is class, 3 is order, 4 is family, 5 is genus and 6 is specie
In qiime2, level 1 is domain, level 2 is phylum, 3 is class, 4 is order, 5 is family, 6 is genus and 7 is specie.
So in my score plot, level 1 in qiime2 that it’s D_0__Bacteria in SILVA isn’t counting (see score plot uploaded --> cause R-value as also p-value are cero but the rest is.
I don’t know if I not importing a good txt or what is happening is a semantic problem between the database format and qiime2 nomenclature.
Will be grateful if someone knows what is the real issue here.