how do you get a boot scan done with MSE AND if you can how to do it?

I had an instance where i had avast. I ran a boot scan and it left a left a trojan "avast boot", but i ran MSE and i cant seem to find a way to be sure that he system is now clean. I wonder if you have some way of being able to run a boot scan right when you have the windows symbol pop up?

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