If so, what issues do I need to be aware of?
We don’t recommend mixing Cell3™ Target enrichment probes with libraries prepared from other library prep kits because, we cannot guarantee the results.
However, if you choose to do this you should be aware that some compatibility issues may arise. For example, the blockers in our kits are designed for our library prep kits and are for hybridisation-based kits with 8nt or lower indexing. Therefore, depending on the kit you used, you may see a high percentage of off target reads.