doRiNA

Database of posttranscriptional regulatory elements and function

Installation

First, install bedtools, we recommend the latest release:

wget https://github.com/arq5x/bedtools2/archive/master.zip -O bedtools.zip
tar -xf bedtools.zip
cd bedtools2-master
make

Then, create a virtual environment and install doRiNA from source:

python3 -m venv dorina-dev
source activate dorina-dev
git clone https://github.com/dieterich-lab/dorina.git
cd dorina
pip install -r requirements.txt -r test_requirements.txt
pip install .

For doRiNA development, please use Python version > 3.4.

Usage

Dorina requires the files to be setup locally. Let /path/to/datasets/ be the the setup path. /path/to/datasets/ should contain :

• /path/to/datasets/regulators
• /path/to/datasets/genomes

Both sub-directories have the same structure:

• /path/to/datasets/genomes/{organism}/{assembly}/
• /path/to/datasets/regulators/{organism}/{assembly}/

Regulators can be obtained from (here)[http://dorina.mdc-berlin.de/regulators]. Each bed file should be accompanied with metadata file with the same name, but the .json extension:

{ "id": "d_melanogaster", "label": "Fly", "scientific": "Drosophila melanogaster", "weight": 3}

The genome directory contains genome annotation separated into several regions for further filtering.

Given the directory structure is correct, the following command should retrieve the miR-1247 regulators of human genome assembly hg19:

dorina run 'hg19' --seta 'hsa-miR-1247|CLASH' -p /path/to/datasets/ > miR-1247.bed

To list the avaiable data sources, use:

dorina genomes -p /path/to/datasets/ | less 
dorina regulators -p /path/to/datasets/ | less

Building an assembly

Please see here

Supported dataset

Regulatory

• RNA Binding Proteins obtained by cross-linking and immunoprecipitation derived experiments (CLIP)
• miRNA–RNA interactions obtained by clash experiments
• Predicted RNA interactions

Expression

Dorina can filter the regulatory datasets by expression

Variation

Retrieves single nucleotide variants co-occurring with regulatory elements

License

dorina is licensed under the GNU General Public Licence (GPL) version 3. See LICENSE file for details.