RegTools
RegTools is a set of tools that integrate DNA-seq and RNA-seq data to help interpret mutations in a regulatory and splicing context. You can find the source code at our GitHub repository or just use our Docker image without need for installation.
Features
- Extract exon-exon junctions from a RNAseq BAM/CRAM 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
For information about the individual RegTools commands, please see the Commands page
Contribute
Citation
You can find a bioRxiv preprint describing our intial validation of RegTools here
Data availability
We have recently applied RegTools to the TCGA data. As part of our commitment to open-access data sharing, we have
made the output files from junctions annotate and cis-splice-effects identify available for download via AWS S3. For information on how to download this data, please refer to our datamed.org entries located here: junctions annotate results and cis-splice-effects identify results
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. Github issues are another option to contact the project about potential bugs.
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.