We have two paired-end sequencing runs using the same target region (V4) but for a different set of samples each, all of them related to the same experiment. We know that there could be technical issues affecting the quality of the obtained reads in each run. We plan to use Dada2 to get our sequence variants.
It is ok to use a different set of trimming parameters for each run? In that case, which Qiime 2 tool can we use to merge the sequence variant tables coming from both runs?
Yes! In fact, it seems most likely that they will need to be slightly different, because they are two different runs. The one caveat here is that the trim-left parameter needs to be the same for each of these runs. This parameter is used primarily for trimming primers, so theoretically you should have the same primer across runs (if not please let me know!).
Take a look at the FMT tutorial for an example of merging multiple runs!
