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I think Sam Worthington was kneeling in the chair, and with computer graphics, they erased the bottom of the wheelchair to make it look like nothing was there. The "skinny legs" are most definately fake, and probably attached to the wheelchair.

Throughout the film, Jake repeatedly moves to his wheelchair to a link chamber, but he's wearing long pants, and we don't see his legs. If you look at him when he's wearing shorts, he never moves much.

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