We run analysis on amplicon quite frequently but there is one dataset that provides weird looking (to us) graph when we run demux view as below.
rawdata.qzv (313.7 KB)
We noticed that for reverse reads, from 50-110 bp the graph looks not normal?
Does this mean that the quality is actually not good?
What we did to the raw data before we imported into QIIME2, we did primer and quality trimming using bbduk. Our previous analysis that used the same workflow did not have problem like this so I doubt it was because of the bbduk trimming.
Appreciate any thoughts about this.