Thanks for the follow up.
My sequence data came from GeneWiz NGS.
The only quality control I performed was before sequencing, so the quality scores should be unmodified. I can reach out to GeneWiz to double check this.
When I open my fatsq files in a text editor (after unzipping), these are the first few lines - I am pretty sure this only uses the ASCII characters, but here it is anyway -
This might not fix anything but I remembered that I did use the raw files as imported data, rather than unzipping then importing. Is this an issue? The zipped files straight from GeneWiz don't use the ASCII characters (that is, when I open them in a text editor before unzipping). Does Q2 do that step for me, or should I go back and unzip each file then import?