you can do this using ffmpeg. you can see the other post (http://khawarblog.blogspot.co.uk/2014/01/video-thumbnails-creating-montage.html) to know how you can install ffmpeg with LGPL license configuration. Once everything is ready, you can use the following command to transcode. For example, you have a test.avi file that you want to convert to flv format.
ffmpeg -i ./test.avi -ar 22050 -ab 32 -f flv avi.flv
It will generate a avi.flv output. However, there will be no sound in this. In order to tackle this issue, you have to reconfigure the ffmpeg with --enable-libmp3lame flag and repeat the installation process.
./configure --disable-gpl --enable-libmp3lame
make
make install
once it is done, you can use the above ffmpeg command and this time audio will work :)
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