You can execute any type of ffmpeg commands using ASP.NET through Media Handler Pro. Please view some examples of how to execute ffmpeg command by using Media Handler Pro.
'// the following line grab 20 thumbnails in jpg format from video sample.avi
MediaHandler _mhandler = new MediaHandler();
_mhandler.FFMPEGPath = HttpContext.Current.Server.MapPath("~\\ffmpeg\\ffmpeg.exe");
_mhandler.CustomCommand = "-i c:\\video\\sample.avi -an -y -f image2 -vframes 20 c:\\video\\sample%d.jpg";
_mhandler.Execute_FFMPEG();
'// the following line grab 20 thumbnails in jpg format from video sample.avi
string outfile = m_handler.Execute_FFMPEG(_ffmpegpath, "-i c:\\video\\sample.avi -an -y -f image2 -vframes 20 c:\\video\\sample%d.jpg");