We obtained a low on-target rate in our experiment (20 – 40%), what could be the problem? What could we do to prevent it? Is it possible to add another quality control step before sequencing?

It is certain that the problem occurred during the hybridization and subsequent wash steps. There could be several causes of the problem. To name a few examples: too low hybridization temperature, hybridization buffer concentration problem, stringent wash temperature or wash buffer concentrations.