deeptools
Link to section 'Introduction' of '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.
Link to section 'Versions' of 'deeptools' Versions
- 3.5.1-py
Link to section 'Commands' of 'deeptools' Commands
- alignmentSieve
- bamCompare
- bamCoverage
- bamPEFragmentSize
- bigwigCompare
- computeGCBias
- computeMatrix
- computeMatrixOperations
- correctGCBias
- deeptools
- estimateReadFiltering
- estimateScaleFactor
- multiBamSummary
- multiBigwigSummary
- plotCorrelation
- plotCoverage
- plotEnrichment
- plotFingerprint
- plotHeatmap
- plotPCA
- plotProfile
Link to section 'Module' of 'deeptools' Module
You can load the modules by:
module load biocontainers
module load deeptools
Link to section 'Example job' of 'deeptools' 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 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