I have filtered table and sequences using qiime2 instruction (frequency-based & mitochondria, chloroplast, Archaea, Eukaryota). However, the dimension of table did not change after using filter and the number of taxa was 854 before and after using filters. Also, the output cladogram shows lots of taxonomy which is not different based on our target variable. Please see the below cladogram. I was wondering if you could please let me know if I miss any step.
Thanks for your reply. Also, I have pasted the commands for quality control (dada2) as well as classifier to assign taxonomy based on SILVA database for any clue. Thanks!
This looks like LEfSe output. If it is, then this is not a true cladogram, despite name of the function. It is merely a dendrogram based on taxonomic ranks, were each node is a taxonomic level. If you do not have | separating the ranks, then you're only ever going to see this "star" cladogram. Where each tip is a unique full taxonomy string.
I'd recommend installing dokdo into your QIIME 2 environment and then run the prepare-lefse command. Then upload to LEfSe Galaxy.