How to ease coughing?

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My almost two years old has a terrible cough at night. I try to make him sit up a bit more but he insists in lying flat on his stomach, obviously making it worse. Are there any safe home remedies or something we can try? Our pediatrician says that over the counter cough medicine aren't proven to work at all and they won't subscribe anything due to him being so little and they also don't think it's bad enough. They only recommended honey in warm water with some milk.