MPRAOligoDesign’s documentation
Welcome!
Workflow to design oligos for MPRA out of regions (and variants).
MPRAOligoDesign is built on top of Snakemake. Insert your code into the respective folders, i.e. scripts, rules, and envs. Define the entry point of the workflow in the Snakefile and the main configuration in a config.yaml file.
- Authors
Max Schubach (@visze) Computational Genome Biology Group Berlin Institute of Health at Charité Universitätsklinikum Berlin
- Usage
If you use this workflow in a paper, don’t forget to give credits to the authors by citing the URL of the (original) repository and, if available, it’s DOI. (see above)
- Installation & Getting Started
Instructions for the Installation of the program and some examples to get you started.
- Project Information
More information on the project, including the changelog, list of contributing authors, and contribution instructions.
Overview
Workflow to gerenate an oligo design for an MPRA experiments. It has mltiple ways to generate sequences:
Variants (vcf) + regions (bed)
Variants (vcf)
Regions (bed)
Sequnces (fasta)
All 4 strategies can be combined latzer into one final design files. This allows you to put controlls as well as your deisgn in one workflow.
When sequences are generated it filters them with multiple check: 1. Homopolymer size (for all) 2. EcoRI or SbfI restriction site (for all) 3. Simple repeats (not pure sequences) 4. TSS site overlap (not pure sequences) 5. CTCF overlap (not pure sequences)
Quick Example
To run MPRAOligoDesign, first activate the snakemake environment with the following command:
conda activate snakemake
And then run the main workflow with:
snakemake --use-conda --cores $N --configfile config/config.yaml
Features
- –use-conda:
This utility uses conda to efficiently query repositories and query package dependencies.
- –cores:
This utility sets the number of cores ($N) to be used by MPRAOligoDesign.
- –configfile:
This file (e.g.,
config/config.yaml) contains the project, its objects and properties, and sub-properties and its objects that must be set before running MPRAOligoDesign.
Feedback
Feel free to leave feedback(s), ask question(s), or report bug(s) at our issues page: MPRAOligoDesign Issues.