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When I try to convert an iOS video from .MOV to .MP4, it comes out upside down. I am guessing that is because Handbrake doesn't respect the iOS Rotate flag...or I don't know which option to set.

Is there a way to fix this problem?

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Why do you want to convert a video from MOV to MP4? Both containers use the H.264 codec and AAC audio, so re-encoding usually isn't necessary. Chances are Handbrake doesn't support it, really, so you need something like here: iPhone recorded videos getting rotated on Windows systems (I know, I already linked you to this a while ago…) –  slhck Dec 9 '13 at 20:52

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