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90 degrees phase difference signals

Question asked by kasapoglu.orkun.001 on Mar 11, 2013
I want to create 2 signals and they must have 90 degrees phase difference (on square wave). for example signals have 2 kHz freq. i set the timer 8 kHz and just changed the one of the outputs on each timer interrupt. the signals are coming 90 degrees difference while i'm debugging on discovery board but when i stop debugging (controller is free running) i'm not seeing the difference between signals just inverted 2 signals on scope. can i do it with pwm or capture/compare mode?