Hi @Laura_Scannell - One thing I'll point out about FastQC is that the x axis on those 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!
