Ofcourse you can perform comet assay in agarose gel elelectrophoresis unit. Make sure that you run the experiment at constant current i.e. 300mA by adjusting the field of 1V per Cm of ur electrophoresis unit.
Voltage is more important than the mA ! Therefore, make sure that your V/cm are correct and then you can perform the comet assay in a normal electrophoresis tank. Remember to adjust the amount of liquid, so that your slides are covered.