text: user4681: 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?
  
  user10379: 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/
  
original_text: 4681: <p>I want to analyse data from a CRISPR/Cas9 screen (control vs. treatment) and I'm using Mageck (<a href="https://sourceforge.net/projects/mageck/" rel="nofollow noreferrer">https://sourceforge.net/projects/mageck/</a>). 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?</p>
   10379: <p>The other answer is incorrect. The original poster is asking about paired-end sequencing data, not paired treatment/control experimental design.</p>
  <p>Here is how you analyze paired-end sequencing data (this was an answer I gave on Biostars last year):</p>
  <p><a href="https://www.biostars.org/p/303656/" rel="nofollow noreferrer">https://www.biostars.org/p/303656/</a></p>
  