MAGeCK Gene Quantify from count file

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MAGeCK Gene Quantify from count file

This module is designed to run MAGeCK command through Array Studio, to generate inference report from the count data. 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

#The first line of command is for the count data generation
#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 module can be accessed by:

Mageck02.png

Installation

For the installation about Mageck package, please refer to the other wiki: MAGeCK Count from Fastq

General

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Input/Output

This function works on count data generated by Mageck, and will require a design file to group the samples into control and treat.

For instance, if user already have the normalized count data generated by the CRISPR | CRISPR Mageck | Mageck Count from Fastq, user can use this as input file.

A desing.txt for example:

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

Options

  • Exe Path:
  • Algorithm:
  • Design File:
  • Output Folder:
  • Output Prefix:


  • CNV Matrix:
  • Norm-Method:
  • Threads:
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Output Results

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

Mageck08.png

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

Mageck04.png

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

Omicscript

MageckTest.oscript

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