pyDNase v0.2.0

pyDNase is a suite of tools for analysing DNase-seq data - pyDNase comes with several analysis scripts covering several common use cases of DNase-seq analysis, and also an implementation of the Wellington, Wellington 1D, and Wellington-boostrap footprinting algorithms.

Accessing the software

To load the module:

$ module load apps/pydnase/v0.2.0

An example command to include in your job script:

python $PYTHON_ROOT/bin/dnase_cut_counter.py <regions> <reads> <output>

This executes dnase_cut_counter.py, the pyDNase script using the BED file named regions, the BAM file reads that contains the DNase-seq data and sending output to the output file.

Accessing Previous Versions

Wherever possible, previous versions of this application will be retained for continuity, especially for research projects that require a consistent version of the software throughout the project. Such versions, however, may be unsupported by IT Services or the applications vendor, and may be withdrawn at short or no notice if they can no longer run on the cluster - for example, essential operating system upgrades may be incompatible with old versions.

At present there are no previous versions of this application on the BlueBEAR service.

Known Problems & Limitations

None.

Other Information

The Support Level for this application is An.

Visit the pyDNase website for more information regarding this application.


Last modified: 7 December 2017


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