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Old 03-26-2013, 08:45 PM   #3
Location: Auckland

Join Date: Sep 2011
Posts: 72

Thanks, very very useful answer

I'm not running 6 samples, that was just a simple example. I'm advising others on a run that hasn't been done yet, it will be a single MiSeq run multiplexed to ~90 samples, with at least 50% PhiX spikes, probably more like 60%. I did rough calculations on the expected number of sequences that we'd get, they correspond with your results (which is good to know). We will also have to use subsampled OTU picking (or at least de novo OTU picking of some kind) since it's not a well studied biome.
Sounds like running it on a desktop is going to be a problem due to memory. Our cluster might just handle it, but only just. Good to catch this problem now. Is there any way you could send me a private message with the email of the collaborator you mentioned, could I contact them?

Last edited by danwiththeplan; 03-26-2013 at 08:48 PM. Reason: clarity
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