Hi @Sue,
Nothing is wrong with your commands - the interactive quality plot looks as expected for sequencing data that's been quality score binned (NovaSeq and iSeq both do this).
You're welcome to cross check the read quality in FastQC, but one thing I'll point out about using FastQC is that the x axis on the plots it generates can be a little confusing if you're directly comparing to q2-demux's summarize visualization, because FastQC actually performs a separate binning of the nt positions:
- FastQC compared to QIIME 2 quality plot
- Quality in reads suddenly decreases with no apparent reason - #5 by thermokarst
So in particular, you're probably looking at a psuedo-log type of plot, where only ~50 or so box plots are displayed, rather than the ~290 box plots that you shared in the screenshot above. Just something worth keeping in mind!
In either case though, you don't need to modify anything you've done up to this point - you're now just using this quality plot to assess the filtering params you'll set when denoising.
Cheers 