Actually, i use Azure Media Streaming services.. (i'm BizSpark), but i suppose AWS has the same services, you just need to include a link, and the service will automaticly encode it into the correct format (don't specify the filetype).

http://azure.microsoft.com/en-us/services/media-services/

https://aws.amazon.com/digital-media/

https://www.google.be/search?q=encode+media+&oq=encode+media...