Purdue University

Commands

• NanoPlot

Module

You can load the modules by:

module load biocontainers
module load nanoplot

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 Nanoplot on our clusters:

#!/bin/bash
#SBATCH -A myallocation     # Allocation name 
#SBATCH -t 1:00:00
#SBATCH -N 1
#SBATCH -n 12
#SBATCH --job-name=nanoplot
#SBATCH --mail-type=FAIL,BEGIN,END
#SBATCH --error=%x-%J-%u.err
#SBATCH --output=%x-%J-%u.out

module --force purge
ml biocontainers nanoplot

NanoPlot --summary sequencing_summary.txt --loglength -o summary-plots-log-transformed  
NanoPlot -t 2 --fastq reads1.fastq.gz reads2.fastq.gz --maxlength 40000 --plots dot --legacy hex
NanoPlot -t 12 --color yellow --bam alignment1.bam alignment2.bam alignment3.bam --downsample 10000 -o bamplots_downsampled