I have run a same set of data with 2 different qiime2 versions: 2018.8 and 2018.11 and i got quite different results for the taxonomy classification. I have tried the classifier produced by both 2018.8 and 2018.11. Therefore, i think the error comes from dada2 files. For the results from 2018.11, there are some remarkable increases of some taxa in some samples which are not the case in the results from 2018.8. I am wondering how it can make such a difference.
I am really confused. Could anyone help to explain this problem?
Thank you so much,