Maximum concentration of adapter dimers?

[Ingeneious]

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?

[jdk787]

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.

[Ingeneious]

Thanks 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.

[GenoMax]

You may lose (significantly) more than 10% data. Short fragments preferentially cluster over longer ones and your adapter dimers would fall in the first category.

[jdk787]

For future samples you could also try diluting your adapters. This would reduce the amount of dimers in your final library and could save you from needing to perform an additional cleanup.

[jdk787]

Thanks 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.

You can get away with more, but you will be losing a significant amount of reads to the dimers. More often than not the cost per reads lost will be more than what the beads would cost.

If you are multiplexing samples you can also perform a cleanup after pooling which could save you some on beads.