What to do if I have both pre-treatment AND WT samples from a CRISPRscreen to analyse

Question

[chrisgr]

I'm trying a crisprscreen analysis using Mageck. I have both pre-treatment(baseline) ánd WT samples (and ofcourse treatment samples). Online I have only found people simply comparing the WT vs treatment. But isn't there a way to include the pre-treatment samples to the command of Mageck in order to normalise the WT and treatment with a baseline first? Or what would be the best approach?

My current command comparing pre-treat vs WT (not including the treatment)

mageck test -k GSE277685_sgRNA_count_table.txt -t Input1_rep1,Input1_rep2 -c WT_week6_rep1,WT_week6_rep2, -n mageck_output/WT/WT_week6

Hope anyone could guide me a bit here

All the best,
Chris

[GenoMax]

You will want to use mageck mle analysis for that.

[chrisgr]

Thank you for your response. I'm confused though. Following this: https://sourceforge.net/p/mageck/wiki/demo/#the-fourth-demo-using-mageck-mle-module

From "The fourth tutorial: using MAGeCK mle module" onward, I would not want to compare the HL60 and KBM7 with their initial samples seperately, resulting in 2 P-values (like in the example), What I want is to compare HL60 and KBM7 with eachother and use their initial samples to normalize.

I want 1 P-value that tells me this gene is different between HL60 and KBM7 while normalized based on their initial samples.

I hope I explain my problem well, let me know and thanks again