Crispritz

Introduction

Crispritz is a software package containing 5 different tools dedicated to perform predictive analysis and result assessement on CRISPR/Cas experiments.

For more information, please check its website: https://biocontainers.pro/tools/crispritz and its home page on Github.

Versions

  • 2.6.5

Commands

  • crispritz.py

Module

You can load the modules by:

module load biocontainers
module load crispritz

Example job

Warning

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 Crispritz on our clusters:

#!/bin/bash
#SBATCH -A myallocation     # Allocation name
#SBATCH -t 1:00:00
#SBATCH -N 1
#SBATCH -n 1
#SBATCH --job-name=crispritz
#SBATCH --mail-type=FAIL,BEGIN,END
#SBATCH --error=%x-%J-%u.err
#SBATCH --output=%x-%J-%u.out

module --force purge
ml biocontainers crispritz

crispritz.py add-variants hg38_1000genomeproject_vcf/ hg38_ref/ &> output.redirect.out

crispritz.py index-genome hg38_ref hg38_ref/ 20bp-NGG-SpCas9.txt -bMax 2 &> output.redirect.out

crispritz.py search hg38_ref/ 20bp-NGG-SpCas9.txt EMX1.sgRNA.txt emx1.hg38 -mm 4 -t -scores hg38_ref/ &> output.redirect.out

crispritz.py search genome_library/NGG_2_hg38_ref/ 20bp-NGG-SpCas9.txt EMX1.sgRNA.txt emx1.hg38.bulges -index -mm 4 -bDNA 1 -bRNA 1 -t &> output.redirect.out

crispritz.py annotate-results emx1.hg38.targets.txt hg38Annotation.bed emx1.hg38 &> output.redirect.out