I use sand in both the run and the coop. I actually use more sand in the coop than the run because of the dirt in the run, I don't think they need as much out there but it is there. Just not as deep.
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We've been using pine shavings for several years and while it is messy,I've found nothing that works quite as well. We use a modified deep litter and a poop board under the roost. The poop board gets cleaned daily and the shavings get changed about 4-6 times a year and we have no smell or other problems.