For performing jitter analysis, typically the oscilloscope should acquire wave forms at the maximum sample rate. Learn about the ramifications of having the horizontal acquisition setup for automatic, constant sample rate, or manual modes.
For many users performing jitter analysis, the manual horizontal mode is the preferred mode of operation. In this mode, rather than changing the horizontal scale to adjust the time duration captured, you select the desired sample rate and then adjust the record length to the desired number of points that will capture some minimum number of unit intervals in the signal.
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