I have slightly different situation.
Run 1: Project A (30 samples) + Project B (45 samples) + Project C (30 samples)
Run 2: Project B (30 samples) + Project D (60 samples).
What would be the best strategy to combine Project B samples from two runs
- qiime mport fastq files for Project B from two runs into one qza file and subsequently process thru DADA2? OR
- Process both runs separately thru DADA2, filter table.qza and rep-seqs.qza samples for project B from each run, merge project B table.qza from two runs and perform subsequent analysis.