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Warning!

Puhti and Mahti computing services have been decommissioned and no new jobs are accepted or executed on its compute nodes. Puhti and Mahti login nodes and storage services are planned to remain available until 15 October 2026. Clean up unnecessary files and move any data you need to keep by 31 August 2026. See the Roihu data migration guide for instructions on transferring your data to Roihu.

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