If you plan to mull the transom window directly to the top of the door, make sure your salesperson knows and provides a factory trim to cover this joint. Or better yet, have the factory mull the door and transom together. This connection can be a tricky one to make on the job.
Building wrap, like Tyvek, should be lapped over so water can't run behind the window. Flashing tape should be used to seal the window's installation flanges to the sheathing. If you are remodeling, install metal head flashing to divert water around the window and pay special attention to caulking.
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