Crispresso2

Introduction

CRISPResso2 is a software pipeline designed to enable rapid and intuitive interpretation of genome editing experiments.

For more information, please check:
Docker hub: https://hub.docker.com/r/pinellolab/crispresso2
Home page: https://github.com/pinellolab/CRISPResso2

Versions

  • 2.2.10

  • 2.2.11a

  • 2.2.8

  • 2.2.9

Commands

  • CRISPResso

  • CRISPRessoAggregate

  • CRISPRessoBatch

  • CRISPRessoCompare

  • CRISPRessoPooled

  • CRISPRessoPooledWGSCompare

  • CRISPRessoWGS

Module

You can load the modules by:

module load biocontainers
module load crispresso2

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 crispresso2 on our clusters:

#!/bin/bash
#SBATCH -A myallocation     # Allocation name
#SBATCH -t 1:00:00
#SBATCH -N 1
#SBATCH -n 1
#SBATCH --job-name=crispresso2
#SBATCH --mail-type=FAIL,BEGIN,END
#SBATCH --error=%x-%J-%u.err
#SBATCH --output=%x-%J-%u.out

module --force purge
ml biocontainers crispresso2

CRISPResso --fastq_r1 nhej.r1.fastq.gz --fastq_r2 nhej.r2.fastq.gz -n nhej --amplicon_seq \
    AATGTCCCCCAATGGGAAGTTCATCTGGCACTGCCCACAGGTGAGGAGGTCATGATCCCCTTCTGGAGCTCCCAACGGGCCGTGGTCTGGTTCATCATCTGTAAGAATGGCTTCAAGAGGCTCGGCTGTGGTT