When to combine Miseq runs?

Commands in mothur
1

Hello,
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.

Thanks.

2

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.

Pat

3

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

4

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.

Pat

5

Thanks!