For more elaborate tasks, you probably want a video editor; but to cut out a single clip, these are the two methods I've been using lately:
1. If you have at least two TiVos: Advance the recording to what you want as the start point. Pause it there. Move to the other TiVo, and select "Transfer from paused point". Stop the transfer when you reach the desired endpoint. You can then move the truncated recording back to the other TiVo, or to your computer.
2. Download and decrypt the whole program. Play it back, and take note of the desired start and end points (or do this on the TiVo). Then, use FFmpeg to copy the desired portion:
ffmpeg -i filename.mpg -ss 1:00:00 -t 5:00 -vcodec copy -acodec copy newfile.ts
This would take a five minute clip, starting an hour into the recording. If the result isn't quite right, you can tweak the numbers and repeat, down to tenths of seconds if necessary. You can also use the TiVo-to-TiVo method to do the initial editing, and fine-tune it with the FFmpeg technique.
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