Thank you for your help, I was able to resolve my problem with this advice.
Less important to my project but I am curious and haven't found a clear answer here - if I tried to import my data as the wrong type (e.g. I have paired end reads with 33 quality score, what if I tried to import as another type instead), would the program continue and try to analyze the data anyways, or does the import process 'check' if the data is in the correct format? I'm also thinking about the demultiplexing steps, if I tried to demultiplex samples that were not multiplexed, would qiime refuse the command or would it make changes to the file?
My lack of experience with the program makes me worry about making accidents like this without realizing, and tainting my downstream analysis.
All methods in the QIIME 2 core distro assume Phred 33 offset - if you import Phred 64 data (using the Phred 64 manifest formats), QIIME 2 will automatically convert the quality scores to phred 33.
The import process doesn't check, this is because it is possible for a dataset to have valid quality scores within both the Phred 64 and Phred 33 ranges, which makes it impossible to distinguish, in certain cases. The demux summarize viz will show you a warning if it thinks you might have picked the wrong range, but again, it can't know for sure in all cases.
It depends! Computers aren't smart or clever - they only do exactly what you tell them to do, so it depends on the commands run, and the data input.
