I was asked to help analyzing an existing microbiome project; however, the sequencing was done in a weird way. Rather than running all samples on a single MiSeq run, they were split across multiple runs. But not by running whole samples on different runs, but by running all samples across three spike-in runs. So for each sample, I have reads from three different runs.
I was planning to analyse the data using DADA2 as usual, but now with having three runs per sample I'm not so sure anymore. I know that separate runs should be run separately through DADA2 due to error modeling. I know how to merge whole samples from different runs, but I have no idea how I could merge separate samples.
Is there a way to save this project? Any suggestions on how to analyse the data?