MAGeCK Count from Fastq

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MAGeCK Count from Fastq

This module is designed to run MAGeCK command through Array Studio, to generate count data from fastq files. Full name of MAGeCK is "Model-based Analysis of Genome-wide CRISPR-Cas9 Knockout", which is developed and maintained by Wei Li and Han Xu from Dr. Xiaole Shirley Liu's lab at Department of Biostatistics and Computational Biology, Dana-Farber Cancer Institute and Harvard School of Public Health.

Many independent studies have adopted MAGeCK to identify important genes from the recent genome-scale CRISPR-Cas9 knockout screens technology, to better assistant our users who are also interested using this computational tool, OmicSoft has designed this GUI so users can easily setup their parameters and send the job to run by MAGeCK in the Linux environment, once the analysis is done, import the result into ArrayStudio GUI for further visualizations/analysis.

Omicsoft implementation is benchmarked with MAGeCK v.0.5.7

mageck count -l library.txt -n demo --sample-label L1,CTRL  --fastq test1.fastq test2.fastq 
#mageck test -k demo.count.txt -t L1 -c CTRL -n demo #This part will be run for MAGeCK "test" command

This module can be accessed by:



Install required packages for MAGeCK

Install MAGeCK

Test Code




This function works on fastq/fastq.gz data, and will require a design file and library file.

For instance, if there are two fastq files for input file:


A desing.txt for example:

FastqFile	SampleLabel	Group
test1.fastq.gz	C1	control
test2.fastq.gz	T1	treat


  • MAGeCK Path:
  • Library File:
  • Design File:
  • Output Folder:
  • Output Prefix:

  • Norm-Method:
  • Reverse Complementary:
  • Trim 5' End:
  • sgRNA Len:
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Output Results

In the ArrayStudio GUI, user will be able to see the result table named as "prefix".sgRNANormalizedCount:


In the output folder, user will be able to see these result files:


For more details about the result files in the output folder, please refer to the Mageck's own wiki: Mageck output



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