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Old 06-28-2017, 04:26 PM   #2
Location: Honolulu, HI

Join Date: Jul 2015
Posts: 40

Hey tugecko,

I'm doing ddRAD as well. Size-selection with beads tends to leave you with a relatively wide range of fragment sizes (folks in my lab do ezRAD quite a bit, and this is the method they most commonly choose). If a tight size-selection is what you're aiming for, I might avoid using beads. And SPRI beads are deceptively expensive in their own right.

Also, I haven't heard of anybody making their own gels for use in the Pippin-Prep. I don't know if you've see one, but it's a pretty complex little cartridge! I don't really think it can be done, to be honest.

As for the manual gel excision, I can't really say I've tried it for ddRAD. But the tighter your range, the greater the risk for allele drop-out. Based on the gels I've run (PCR, PCR product excision, etc.), I wouldn't be inclined to trust it. But I'm pretty sure there are papers published where people have done just that, so they must be much better at running gels than I am! I bet they had really nice gel-rigs.

Good luck!

- Sean
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