pybedtools 0.7.10

pybedtools is a Python wrapped for BEDTools. The BEDTools utilities are a swiss-army knife of tools for a wide-range of genomics analysis tasks. The most widely-used tools enable genome arithmetic: that is, set theory on the genome. For example, BEDTools allows one to intersect, merge, count, complement, and shuffle genomic intervals from multiple files in widely-used genomic file formats such as BAM, BED, GFF/GTF, VCF. While each individual tool is designed to do a relatively simple task (e.g., intersect two interval files), quite sophisticated analyses can be conducted by combining multiple bedtools operations.

Accessing the software

There are 2 modules available for this version of pybedtools, one with Python 2 and one with Python 3. Load the one that is relevant to your needs:

$ module load pybedtools/0.7.10-iomkl-2018a-Python-2.7.14

pybedtools is a Python package. It needs to be imported into your Python script to be used:

import pybedtools

<pybedtools commands>

Example: pybedtools Job

An example can be found at ${BB_EXAMPLES}/pybedtools/0.7.10/ The example can be copied to a test directory and submitted to the batch system using sbatch.

$ cp -r ${BB_EXAMPLES}/pybedtools/0.7.10 ~/pybedtools-0.7.10-test
$ cd ~/pybedtools-0.7.10-test

Edit the script according to your needs, then do:

$ sbatch

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.

Previous versions of this application are recorded below:

Known Problems & Limitations


Other Information

The Support Level for this application is An.

Visit the pybedtools website for more information regarding this application.

Last modified: 11 January 2019


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