A droplet actuation system is provided including a droplet actuation device including a substrate that includes electrodes for conducting droplet operations; temperature control means for heating and/or cooling a region of the droplet actuation device and arranged such that a droplet can be transported on the electrodes to a region for heating; and a means for effecting a magnetic field in proximity to one or more of the electrodes sufficient to immobilize magnetically responsive beads in a droplet on the substrate during droplet operations. The system further includes a processor for controlling the electrodes and temperature control means, wherein the processor is programmed, and electrodes and magnetic field are arranged, to cause the electrodes to split a droplet including the magnetically responsive beads yielding a first daughter droplet which includes the magnetically responsive beads and a second daughter droplet without a substantial amount of the magnetically responsive beads.