I'm dealing with a PWM generator which drives a load at 12V with pretty high currents (5-10A) The PWM frequency is in the band of 100-200 Hz. Which is the best choice and right configuration of ferrite beads to achieve the best filtering of EMI?
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Ferrite beads will prove fairly useless at such a low frequency. They tend to start becoming useful in the area above 10 MHz. I'd consider LC filtering but the precise way depends on your particular circuit. Here's some general info on ferrite beads: