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?
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):