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Encoding software

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Helmet:
Can someone recommend some encoding software which allow to choose specs like Codec Format, Level Profile (for video codec format), Number of Frames, Bitrate, etc?

More specifically, I would need something which allow me to change the specs for those mkv files I want to play on my blu-ray player, like the video codec Profile Level or to change the default audio or subtitle streams (for instance, if one mkv comes with the default audio stream in english, to change it to japanese).

I already have and use MediaCoder, but I would like to have some alternatives, as MediaCoder is sometimes a bit too complex (and also, while freeware, their pestering about donations is annoying like hell).

Tri_Edge:
If you want simplicity just use Handbrake.

Mcgreag:
MeGUI would be the usual recommended software but it might be too complex for you.

Helmet:
HandBrake is a good option. Any other suggestions?

I have one problem though during encoding: when I try to convert ogm files to mkv, it never keeps the subtitles, regardless of what tool I use, HandBrake or MediaCoder. Does anyone have any idea why?

Krudda:
Well, it looks like you want this for re-coding, more than encoding.
I would suggest XMedia-Recode
This program has all the options you are looking for and can convert to Almost 50 formats (that's including audio formats)
The batch encode crashes on me constantly, but other than that, superb converter.
I seriously suggest giving it a test run, its faster and more reliable than Handbrake and certainly easier than megui.
Also, what do you mean by "keep" the subtitles?
Burn them into the video or keep the soft option in the file or what?
If you want the subtitles for on a dvd or bluray, you will need to convert them to an appropriate format for dvd/bluray
I do not suggest using xmedia recode's inbuilt hardcode/soft sub feature, as it is imperfect. (though it will work)

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