Question on CRISPR screen analysis

[Ashwin Iyer]

Hello all, 

I have a FACS based CRISPR screen for which I can compare the sorted sample with presort. I also have a negative control arm of the screen with the same presort but with a different sorted population. Traditionally, it makes sense to compare the sorted population to the presort but how can I also normalize it to the negative control arm of the screen? 

Can someone please help me or suggest softwares that can carry out this type of analysis? 

Thanks, 
Ashwin Iyer