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