Closed:MAGeCK normalization; during count, test or both?

Question

[sonark]

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Hello, I am new to using MAGeCK for CRISPR/Cas9 knockout screens.

I have control sgRNAs that are non-targeting, and I wish to use them for normalization using the --norm-method control and --control-sgrna options. However, it confuses me that I have this normalization option in both the count and the test or mle steps. Am I supposed to normalize by my non-targeting controls in every step? Both during counting AND during testing?

I would be grateful for some guidance. Thank you

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