I am using Qiime2 version 2020.6 currently. I merged processed samples(after DADA2) samples from 2 runs using the following command:
qiime feature-table merge
--i-tables table2.qza \
qiime feature-table merge-seqs
--i-data rep-seqs2.qza \
When I ran the distance matrix ordination using bray curtis and Unweighted Unifrac, I found that samples from both the run formed distinct groups. See below:
After merging, I created a rooted-tree based on the merged table. Since we normally outsource our samples for sequencing, I am unsure if this group could be due to difference in sequencing parameter. I usually do 100000 reads/sample. I am not sure what is causing this. Please advise.