crispresso2
Link to section 'Introduction' of 'crispresso2' Introduction
CRISPResso2 is a software pipeline designed to enable rapid and intuitive interpretation of genome editing experiments.
Docker hub: https://hub.docker.com/r/pinellolab/crispresso2
Home page: https://github.com/pinellolab/CRISPResso2
Link to section 'Versions' of 'crispresso2' Versions
- 2.2.10
- 2.2.11a
- 2.2.8
- 2.2.9
Link to section 'Commands' of 'crispresso2' Commands
- CRISPResso
- CRISPRessoAggregate
- CRISPRessoBatch
- CRISPRessoCompare
- CRISPRessoPooled
- CRISPRessoPooledWGSCompare
- CRISPRessoWGS
Link to section 'Module' of 'crispresso2' Module
You can load the modules by:
module load biocontainers
module load crispresso2
Link to section 'Example job' of 'crispresso2' 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 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