Export the signal from your scope as CSV. You can import this CSV in almost any mathematics package (eg. MATLAB) or programming language (eg. Python). The learning curve for both will be quite steep if you've never used them before. If you're into NI products, you could probably do this in SignalExpress. Including capturing it from the scope and down sampling. You could even import it into the abomination called Excel.
You could skip samples or do some averaging to sample it down to the desired sampling rate. Fancier algorithms might first reconstruct the signal and resample this reconstructed signal. It depends on the ratio between original sampling rate and desired sampling rate, and the desired fidelity.