<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>

CC BY-SA 4.0
2021-04-08T18:54:40.870Z
2021-04-08T18:54:40.870Z
Yenaled
<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>

<ngs><crispr>
CRISPR/Cas9 screen analysis with Mageck: paired-end sequencing
# 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

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## 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/>


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