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deepTools

deepTools is a suite of tools for exploring deep-sequencing data. It handles the large amounts of data generated by DNA sequencing and is widely used for normalising, comparing and visualising coverage from ChIP-seq, RNA-seq and related assays. It includes tools such as bamCoverage, bamCompare, computeMatrix, plotHeatmap and plotProfile.

License

Free to use and open source under GNU GPLv3.

Available

  • Roihu: 3.5.3 (module py-deeptools), via the bio-apps module.

Usage

deepTools is part of the bio-apps collection on Roihu. Load the bio-apps module tree and then the module:

module load bio-apps/v202603
module load py-deeptools/3.5.3

For example, to generate a normalised coverage track from an indexed BAM file:

bamCoverage -b aligned.sorted.bam -o coverage.bw --normalizeUsing RPKM -p 8

Example batch script

#!/bin/bash
#SBATCH --job-name=deeptools
#SBATCH --account=<project>
#SBATCH --output=output_%j.txt
#SBATCH --error=errors_%j.txt
#SBATCH --partition=small
#SBATCH --time=04:00:00
#SBATCH --nodes=1
#SBATCH --ntasks=1
#SBATCH --cpus-per-task=8
#SBATCH --mem-per-cpu=2G

module load bio-apps/v202603
module load py-deeptools/3.5.3

bamCoverage -b aligned.sorted.bam -o coverage.bw --normalizeUsing RPKM -p $SLURM_CPUS_PER_TASK

Replace <project> with your CSC project (for example project_2001234).

See creating a batch job script for Roihu for more information about running batch jobs.

Support

CSC Service Desk

More information