Hi

I remember reading about a library called the PRU, u might want to give it a try.

This link might give u some starting point, http://www.element14.com/community/community/designcenter/single-board-computers/next-gen_beaglebone//blog/2013/08/04/bbb--high-speed-data-acquisition-and-web-based-ui

Hi,

be careful, if you need accurate data, ideally you should provide a dedicated system to acquire your signal with no OS used. Over an OS is challenging to make sure an high accuracy of data and low jitter even though using interrupt handlers.

Regarding high sampling rates I would suggest you to find out further informations within Beaglebone's datasheet.