Sorry to follow up so late about this, but I have two more questions regarding this last statement:
As as noted in the thread you linked, each run can be slightly different in terms of its quality, you can use slightly different truncation parameters (not trim parameters) for each run to get the reads to merge.
Just to clarify, does this mean I can use different quality score "thresholds" to inform truncation decisions (e.g. trunc the sequence base where q<30 for one run, but use q<25 for another run?). I assumed yes based on posts like this one, but I just wanted to make sure I'm not misinterpreting what you had said.
Also, is it still acceptable to use different quality score thresholds to inform truncation decisions if two runs contain the same set of samples and I will be combining the actual sequence data for each sample ID (e.g. using: qiime feature-table merge with the --p-overlap-method sum parameter)?
Thank you!