EpiDiverse/dmr is a bioinformatics analysis pipeline for calling differentially methylated positions or regions from non-model plant species.
The workflow processes raw methylation data from bedGraphs resulting from the EpiDiverse/wgbs pipeline, which are then grouped for analysis with bedtools unionbedg. Each pairwise comparison between groups is performed with metilene, and downstream visualisation is carried out with R-packages ggplot2 and gplots to produce distribution plots and heatmaps.
See the output documentation for more details of the results.
The pipeline is built using Nextflow, a workflow tool to run tasks across multiple compute infrastructures in a very portable manner. It comes with docker containers making installation trivial and results highly reproducible.
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Install
nextflow -
Install one of
docker,singularityorconda -
Download the pipeline and test it on a minimal dataset with a single command
NXF_VER=20.07.1 nextflow run epidiverse/dmr -profile test,<docker|singularity|conda>- Start running your own analysis!
NXF_VER=20.07.1 nextflow run epidiverse/dmr -profile <docker|singularity|conda> \
--input /path/to/wgbs/bam --samples /path/to/samples.tsvSee the usage documentation for all of the available options when running the pipeline.
The EpiDiverse/dmr pipeline is part of the EpiDiverse Toolkit, a best practice suite of tools intended for the study of Ecological Plant Epigenetics. Links to general guidelines and pipeline-specific documentation can be found below:
- Installation
- Pipeline configuration
- Running the pipeline
- Understanding the results
- Troubleshooting
These scripts were originally written for use by the EpiDiverse European Training Network, by Adam Nunn (@bio15anu) and Nilay Can (@nilaycan).
This project has received funding from the European Union’s Horizon 2020 research and innovation programme under the Marie Skłodowska-Curie grant agreement No 764965
If you use epidiverse/dmr for your analysis, please cite it using the following doi: