peakranger
Link to section 'Introduction' of 'peakranger' Introduction
Peakranger is a multi-purpose software suite for analyzing next-generation sequencing (NGS) data.
For more information, please check its website: https://biocontainers.pro/tools/peakranger and its home page: http://ranger.sourceforge.net.
Link to section 'Versions' of 'peakranger' Versions
- 1.18
Link to section 'Commands' of 'peakranger' Commands
- peakranger
Link to section 'Module' of 'peakranger' Module
You can load the modules by:
module load biocontainers
module load peakranger
Link to section 'Example job' of 'peakranger' 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 Peakranger on our clusters:
#!/bin/bash
#SBATCH -A myallocation # Allocation name
#SBATCH -t 1:00:00
#SBATCH -N 1
#SBATCH -n 1
#SBATCH --job-name=peakranger
#SBATCH --mail-type=FAIL,BEGIN,END
#SBATCH --error=%x-%J-%u.err
#SBATCH --output=%x-%J-%u.out
module --force purge
ml biocontainers peakranger
peakranger ccat --format bam 27-1_sorted_MDRD_MQ30filtered.bam 27-4_sorted_MDRD_MQ30filtered.bam \
ccat_result_with_HTML_report_5kb_region --report \
--gene_annot_file refGene.txt --plot_region 10000