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I want to show subtitles with my web player (it supports Flash and HTML5). I'm using the MP4 format and I can add subtitles to the player with an external SRT file, but I want to embed subtitle to my mp4 videos.

I can embed subtitles with mp4box (Windows command line tool) or the YAMB program. My desktop media player can see the subtitles but not all of them. I tried to use MeGui, put my MP4 and videos in it and select forced and default subtitle option. Then I started the program without re-encoding. It took several minutes. After this, the MeGui program is turning my MP4 to MKV without re-encoding and made my subtitle forced and default. All players can see the subtitles now, but that is not what I want, I need MP4 format. I tried to make the subtitles forced and default and make the output a MP4 with MeGui, this time the program is encoding my mp4 to MP4.

Is there anyway to embed subtitle to mp4 without re-encoding? My player can display Text Tracks embedded into MP4 files. How can I show my subtitles with my player?

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If you want soft subs as a separate track yes. Easiest way is to use FFMPEG and mov_text:

c:\<PathToFFMPEG>\ffmpeg.exe" -i "c:\<PathToVideo>\video.mp4 -i "c:\<PathToSubs>\video.srt" -c:v copy -c:a copy -c:s mov_text -metadata:s:s:0 language=eng -map 0:0 -map 0:1 -map 1:0 "c:\<PathToVideo>\VideoNew.mp4

Change c:\<PathTo...>\... or drag and drop on cmd screen and it will add for you.

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