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I want to analyse data from a CRISPR/Cas9 screen (control vs. treatment) and I'm using Mageck (https://sourceforge.net/projects/mageck/). The problem is that I'm working with paired-end sequencing data, do I have to analyse R1 and R2 fastq files separately or is possible to do it at same time with Mageck?

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The other answer is incorrect. The original poster is asking about paired-end sequencing data, not paired treatment/control experimental design.

Here is how you analyze paired-end sequencing data (this was an answer I gave on Biostars last year):

https://www.biostars.org/p/303656/

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