Peakranger

Introduction

Peakranger is a multi-purporse 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.

Versions

1.18

Commands

peakranger

Module

You can load the modules by:

module load biocontainers
module load peakranger

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 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