The best way to do it is to upload using MPEG4 with the h.264 codec, with a high bitrate. When YouTube converts your file into flash the quality tends to decrease, so if you REALLY wanted the best quality possible, 15mbit is what the likes of EA Games use on YouTube. Practically, depending on your resolution size something between 7-10mbit is best. This means you can distribute the file as a HD download, as well as saving on upload time and file size
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