Public | Automated Build

Last pushed: a month ago
Short Description
Integrate DNA/RNA-seq data to interpret regulatory and splicing mutations
Full Description



regtools

Tools that integrate DNA-seq and RNA-seq data to help interpret mutations
in a regulatory and splicing context.

Features

  • Identify evidence for aberrant splicing in RNA reads near a list of variants.
  • Extract exon-exon junctions from a RNAseq BAM file.
  • Annotate exon-exon junctions with information from a known transcriptome.
  • Annotate variants with splice-region(the definition of this region is configurable) annotations.

Installation

Clone and install regtools by running:

    git clone https://github.com/griffithlab/regtools
    cd regtools/
    mkdir build
    cd build/
    cmake ..
    make

For convienience we also maintain a docker image available at https://hub.docker.com/r/griffithlab/regtools/

Usage:

    regtools --help

Contribute

  • Issue Tracker: github.com/griffithlab/regtools/issues
  • Source Code: github.com/griffithlab/regtools

Support

If you have issues using the project, please let us know.
We have a mailing list located at: regtools@googlegroups.com and the
forum is here - https://groups.google.com/forum/#!forum/regtools.
Github issues are another option to contact the project about
potential bugs.

Documentation

The documentation for the project is hosted on
Read the Docs.

If you would like to build the documentation locally, please install
mkdocs, pip install mkdocs --user should
work on most machines. Then run mkdocs serve from within the regtools
base directory.

Acknowledgements

Regtools uses several open-source libraries. We would like to thank the
developers of htslib and bedtools. We would also like to thank Travis Abbott for
useful comments and code.

License

The project is licensed under the MIT license.

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griffithlab
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