When to combine Miseq runs?

I have about 6-8 Miseq runs that I need to combine. I’m wondering when it is advisable to combine the data? Or should I just ensure QC parameters are the same between all runs? p.s. each run also has a mock community co-sequenced.


We actually make a files file that contains all of the data in one file. Then all of the data are run together through the entire pipeline.


So doing it that way, do we just get an overall error rate, or can we still get error rates for each miseq run?

When you run get.seqs before seq.error, you could specify each run’s group name separately (assuming you name them differently) and then run get.seqs/seq.error multiple times.