You could demux with tsMuxerGUI. Convert the audio if needed, Mux to MP4 with My Mp4box GUI.
Currently, I have several 1080i TS files, but I'd like to convert them to MP4. All the files are 25fps, but on Handbrake, I change the framerate to 50fps and have Constant Framerate checked. The other setting are on default. I'm not sure I'm getting the best out of the conversion though, and would appreciate any help.
I've tried muxing/demuxing but none of those options seem to work with my TS files. Preferably, I'd like something similar to MKV to MP4 where the audio stream is the only thing converted (is that right?).
You could demux with tsMuxerGUI. Convert the audio if needed, Mux to MP4 with My Mp4box GUI.
Or MkvToolnix to remux to MKV, then MKVtoMP4.
In my PowerShell script Vid2Mp4, the "high quality" Handbrake settings are:
'-e x264 -q 20 --cfr -a 1 -E copy --audio-copy-mask aac,mp3 --audio-fallback faac -B 192 --crop 0:0:0:0 --strict-anamorphic --decomb -x b-adapt=2:rc-lookahead=50'
Constant Framerate is used at the existing rate (25). The purpose of the script is making videos Chromecast compatible, so AAC and MP3 audio is passed through. Otherwise, audio is converted to AAC.
Vid2Mp4: http://forum.videohelp.com/threads/379314-Convert-Videos-for-Playing-on-Chromecast-PowerShell-script