Hi all,
I'm planning on running ddRAD on 1 plate of 96 individuals. I want to pool all of the individuals into one lane of HiSeq (I've done the calculations to figure out coverage etc, and it's fine because my organism has a small genome).
My question is this: why does everyone use 48 barcoded adapters and 2 indices for their 96 individuals? The adapters are much more expensive than barcodes. Is there a reason why I couldn't/shouldn't use, say, 8 barcoded adapters and 12 indices?
I'm planning on running ddRAD on 1 plate of 96 individuals. I want to pool all of the individuals into one lane of HiSeq (I've done the calculations to figure out coverage etc, and it's fine because my organism has a small genome).
My question is this: why does everyone use 48 barcoded adapters and 2 indices for their 96 individuals? The adapters are much more expensive than barcodes. Is there a reason why I couldn't/shouldn't use, say, 8 barcoded adapters and 12 indices?
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