DeepTools

Introduction

DeepTools is a collection of user-friendly tools for normalization and visualization of deep-sequencing data.

For more information, please check its website: https://biocontainers.pro/tools/deeptools and its home page on Github.

Versions

• 3.5.1-py

Commands

• alignmentSieve

• bamCompare

• bamCoverage

• bamPEFragmentSize

• bigwigCompare

• computeGCBias

• computeMatrix

• computeMatrixOperations

• correctGCBias

• deeptools

• estimateReadFiltering

• estimateScaleFactor

• multiBamSummary

• multiBigwigSummary

• plotCorrelation

• plotCoverage

• plotEnrichment

• plotFingerprint

• plotHeatmap

• plotPCA

• plotProfile

Module

You can load the modules by:

module load biocontainers
module load deeptools

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 DeepTools on our clusters:

#!/bin/bash
#SBATCH -A myallocation     # Allocation name
#SBATCH -t 1:00:00
#SBATCH -N 1
#SBATCH -n 4
#SBATCH --job-name=deeptools
#SBATCH --mail-type=FAIL,BEGIN,END
#SBATCH --error=%x-%J-%u.err
#SBATCH --output=%x-%J-%u.out

module --force purge
ml biocontainers deeptools

bamCoverage  --normalizeUsing CPM -p 32  \
     --effectiveGenomeSize  11000000  \
     -b WT_coord_sorted.bam  \
     -o WT_coord_sorted.bw