If you're not quantitating via qPCR, you run the risk of this issue as discussed above:
It's hard to say definitively that this is why your cluster densities are low, but if the problem is not with the library prep kits or with your MiSeq reagents, then library quantitation is worth looking at. I understand that you've not had problems with other libraries, but maybe there's something about the Sureselect method that causes it to be less efficient. qPCR would tell you for sure one way or the other if that was your problem.
Originally posted by pmiguel
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