video captured from iphone gets rotated when converted to .mp4 using ffmpeg

Question

When I try to upload videos captured from my iPhone in my app, the server performs a conversion from .mov to .mp4 so that it can be played in other platforms. However the problem is that when I shoot the video (in portrait orientation) and it is converted (using ffmpeg) and then played back from the server, it appears to be rotated. Any idea?