Answers.Body: <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>
  
Answers.ContentLicense: CC BY-SA 4.0
Answers.CreationDate: 2021-04-08T18:54:40.870Z
Answers.LastActivityDate: 2021-04-08T18:54:40.870Z
Answers.UserDisplayName: Yenaled
Body: <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>
  
Tags: <ngs><crispr>
Title: CRISPR/Cas9 screen analysis with Mageck: paired-end sequencing
ThreadText: # CRISPR/Cas9 screen analysis with Mageck: paired-end sequencing
  
  (Asked by: username_0 on 2019-11-12)
  
  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?
  
  **Tags:** ngs, crispr
  
  
  ---
  
  ## 1 answers
  
  ### Answer by username_1 on 2021-04-08. Score: 1
  
  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/>
  
  
  ---
  
  