#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
##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.