mageck
Link to section 'Introduction' of 'mageck' Introduction
Model-based Analysis of Genome-wide CRISPR-Cas9 Knockout (MAGeCK) is a computational tool to identify important genes from the recent genome-scale CRISPR-Cas9 knockout screens (or GeCKO) technology.
Docker hub: https://hub.docker.com/r/davidliwei/mageck
Home page: https://bitbucket.org/liulab/mageck/src/master/
Link to section 'Versions' of 'mageck' Versions
- 0.5.9.5
Link to section 'Commands' of 'mageck' Commands
- mageck
- mageckGSEA
- RRA
Link to section 'Module' of 'mageck' Module
You can load the modules by:
module load biocontainers
module load mageck
Link to section 'Example job' of 'mageck' Example job
Using #!/bin/sh -l as shebang in the slurm job script will cause the failure of some biocontainer modules. Please use #!/bin/bash instead.
To run mageck on our clusters:
#!/bin/bash
#SBATCH -A myallocation # Allocation name
#SBATCH -t 1:00:00
#SBATCH -N 1
#SBATCH -n 1
#SBATCH --job-name=mageck
#SBATCH --mail-type=FAIL,BEGIN,END
#SBATCH --error=%x-%J-%u.err
#SBATCH --output=%x-%J-%u.out
module --force purge
ml biocontainers mageck
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