If the accident was not your fault, and you have decided to go through your own insurance company to recover the loss, then you'll be expected to pay the deductible on your policy. (This is the reason many people are turned off to the idea of using their own insurance policy, though it's perfectly acceptable to request that your own insurance company repair your vehicle or determine whether or not it's a total loss.) However, assuming the other party is 100% at fault, you'll get your deductible back from the other person's insurance company, although you may need to wait awhile for this to happen.
Sometimes your insurance company can call the other company and request that they pay the deductible up front so that you don't have to pay out of pocket. Since the other company knows they'll be paying it sooner or later, it's highly likely they'll agree to pay the deductible now. You simply need to inquire about this when talking to your adjuster.
If you were placed 20% at fault for the accident, and you're using your own insurance company, then you would recover 80% of your deductible. The comparative negligence is counted against you for whatever percent of fault is assigned to you in the accident.