the best advice I can telll you is to cut it deep enough to use a 45 ell and a 45 street ell it down along the joist to your trap. That works reall well to conserve the wood. Depending on wether you are useing a plastic drain , or the drain is manufactured into the unit already.
the other thing I can tell you is to cut it liberal enough that the 45 or the trap is not really stressed or pressing against the wood or the shower base in any way.
The reason for this is once you put the shower in, you dont want the plastic to "creak" or rub against the wood whenever anyone steps into the shower and stands directly on the drain.
Have that happen to you on a giant re-model only to find out after you are 100% completely done.that the floor sweaks and creaks when someone takes a shower. ...now ..thats a real joy.