You can use the recycled paper pellets(Yesterday's News) but clay cat litter will mess up their respiratory tracts. You ever held your head in a cat box and breathed deeply while the dust is everywhere? It's not fun and you can't breathe afterwards.
I would use aspen(or a mix of aspen and yesterday's news) and increase ventilation. It should help immensely, both the smell and the rats' breathing. Ammonia is one of the major causes of respiratory distress in rats.





