I have around 10% adapter dimers, relative to the molarity of my target product, in my final library. I am trying to avoid another cleanup to reduce costs. What are the maximum amount of adapter dimers you have run with? Should I expect to lose about 10% of my reads?
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I wouldn't sequence libraries that were much more than 2 or 3% dimer.
Also, keep in mind that the dimers will cluster much more efficiently than your library so you will lose closer to 20 to 30% of your reads.
So I guess you have to decide if you want to spend a little extra money on another cleanup or spend money sequencing dimers.Josh Kinman
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Originally posted by Ingeneious View PostThanks for the advice. Have you sequenced with that much? I have seen that recommendation on the boards, but wondering if I could get away with more.
This would be for more than a single experiment or I would happily do another cleanup.
If you are multiplexing samples you can also perform a cleanup after pooling which could save you some on beads.Josh Kinman
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