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I'm working with an Atmel SAM4 ARM Cortex M4 microcontroller and every example I've seen using USB CDC mode bridges a UART channel, and it looks like checks the UART's registers to read the data. Is it possible to have a USB CDC that doesn't interact with the UART so I can actually use that UART channel separtely from the USB CDC as a UART on the separate pins of the MCU? Is this usually how USB CDC is implemented or am I missing something?

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Is it possible to have a USB CDC that doesn't interact with the UART so I can actually use that UART channel separtely from the USB CDC as a UART on the separate pins of the MCU?

Of course. Your microcontroller can do whatever it wants with the data that's sent over USB; bridging it to a UART just happens to be a really obvious and easy-to-implement example.

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