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https://github.com/griffithlab/regtools

Integrate DNA-seq and RNA-seq data to identify mutations that are associated with regulatory effects on gene expression.
https://github.com/griffithlab/regtools

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Integrate DNA-seq and RNA-seq data to identify mutations that are associated with regulatory effects on gene expression.

Host: GitHub
URL: https://github.com/griffithlab/regtools
Owner: griffithlab
License: mit
Created: 2015-05-18T20:46:35.000Z (over 9 years ago)
Default Branch: master
Last Pushed: 2024-08-21T03:30:14.000Z (3 months ago)
Last Synced: 2024-08-21T04:36:39.918Z (3 months ago)
Language: C++
Homepage: https://regtools.readthedocs.org
Size: 6.07 MB
Stars: 115
Watchers: 14
Forks: 26
Open Issues: 34
Metadata Files:
- Readme: README.md
- License: LICENSE

Awesome Lists containing this project

README

![Build Status](https://github.com/griffithlab/regtools/actions/workflows/cmake.yml/badge.svg?branch=master)
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# 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.

## Hardware requirements
RegTools requires only a standard computer with enough RAM to support the in-memory operations.

## Software requirements
OS Requirements
This package is supported for macOS and Linux. The package has been tested on the following systems:

macOS: macOS 10.12 (Sierra), macOS 10.13 (High Sierra), macOS 10.14 (Mojave), macOS 10.15 (Catalina), macOS 11 (Big Sur), macOS 12 (Monterey)

Linux: Ubuntu 16.04, Ubuntu 18.04, Ubuntu 20.04

## Installation

Clone and install regtools by running the following:
```
git clone https://github.com/griffithlab/regtools
cd regtools/
mkdir build
cd build/
cmake ..
make
```

Installation should take 1-5 minutes.

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

## Usage:

```
regtools --help
```

If one wishes to test their installation, we include test data under `test_data`.

Here's an example command using that data along with the example output. This should run in under a minute.

```sh
regtools cis-splice-effects identify -s RF -e 10 -i 10 test_data/HCC1395_chr22.vcf.gz test_data/HCC1395_tumor.bam test_data/chr22_with_ERCC92.fa test_data/chr22_with_ERCC92.gtf

Variant 22 42129188 42129189 -1
Variant region is 22:42128784-42130813

chrom start end name score strand splice_site acceptors_skipped exons_skipped donors_skipped anchor known_donor known_acceptor known_junction gene_names gene_ids transcripts variant_info
position = 22:42125408-42125409
position = 22:42130565-42130566
22 42125407 42130567 JUNC00000001 4 + GT-AG 0 0 0 D 1 0 0 NDUFA6-AS1 ENSG00000237037 ENST00000439129 22:42129188-42129189
position = 22:42128881-42128882
position = 22:42129670-42129671
22 42128880 42129672 JUNC00000002 3 + GT-AG 0 0 0 N 0 0 0 NA NA NA 22:42129188-42129189
position = 22:42128944-42128945
position = 22:42129031-42129032
22 42128943 42129033 JUNC00000003 4 - GT-GG 1 0 0 D 1 0 0 CYP2D6 ENSG00000100197 ENST00000360608,ENST00000389970,ENST00000488442 22:42129188-42129189
position = 22:42129783-42129784
position = 22:42143453-42143454
22 42129782 42143455 JUNC00000004 2 + GC-AG 9 8 9 N 0 0 0 NA NA NA 22:42129188-42129189
position = 22:42130224-42130225
position = 22:42130565-42130566
22 42130223 42130567 JUNC00000005 2 + GT-AG 0 0 0 N 0 0 0 NA NA NA 22:42129188-42129189
```

## 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: [email protected] 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.](https://regtools.readthedocs.org/en/latest/)

If you would like to build the documentation locally, please install
[mkdocs](http://www.mkdocs.org/), `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](https://opensource.org/licenses/MIT).

## Stable release with DOI

[![DOI](https://zenodo.org/badge/35841695.svg)](https://zenodo.org/badge/latestdoi/35841695)