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You may be leading a bit with the knees when you squat. Any time I have people with knee pain while squatting I head to the box squat just at or slightly below parallel and see if they can keep their shins vertical as they sit back deep into the squat. Smash the quads side to side just above the knee cap to about mid way up as well. Some voodoo flossing above the knee cap may be helpful as well. But as always check your squat pattern first with the box squatting before you decide if you knee to do any of the soft tissue work.