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.

• deepTools
  • License
  • Available
  • Usage
    • Example batch script
  • Support
  • More information

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

• deepTools documentation

Do you find this page useful?

Yes

Thank you for your feedback!

No

Thank you! Your feedback is appreciated.

Please let us know how we could improve this page by contacting us or by creating an issue in GitHub. You can also edit this page yourself and contribute your improvements by creating a pull request.