nf-core/mtdmr is a bioinformatics pipeline designed to identify Differentially Methylated Regions (DMRs) across multiple tissues. This end-to-end pipeline processes BAM files to generate comprehensive DMR tables. The pipeline includes several key steps:
- Methylation Calling: Identification of methylation sites and levels.
- DMR Detection: Run metilene to detect regions with significant methylation differences.
- Output Generation: Creation of detailed reports and tables summarizing the DMRs.
The pipeline is highly configurable and can be adapted to various experimental designs and datasets. It leverages the power of Nextflow and Singularity to ensure reproducibility and scalability across different computing environments.
Note
If you are new to Nextflow and nf-core, please refer to this page on how to set-up Nextflow.Make sure to test your setup with -profile test before running the workflow on actual data.
Now, you can run the pipeline using:
nextflow run nf-core/mtdmr \
-profile singularity \
--input samplesheet.csv \
--outdir <OUTDIR>Warning
Please provide pipeline parameters via the CLI or Nextflow -params-file option. Custom config files including those provided by the -c Nextflow option can be used to provide any configuration except for parameters; see docs.
For more details and further functionality, please refer to the usage documentation and the parameter documentation.
To see the results of an example test run with a full size dataset refer to the results tab on the nf-core website pipeline page. For more details about the output files and reports, please refer to the output documentation.
nf-core/mtdmr was originally written by vanreality.
We thank the following people for their extensive assistance in the development of this pipeline:
If you would like to contribute to this pipeline, please see the contributing guidelines.
For further information or help, don't hesitate to get in touch on the Slack #mtdmr channel (you can join with this invite).
An extensive list of references for the tools used by the pipeline can be found in the CITATIONS.md file.
You can cite the nf-core publication as follows:
The nf-core framework for community-curated bioinformatics pipelines.
Philip Ewels, Alexander Peltzer, Sven Fillinger, Harshil Patel, Johannes Alneberg, Andreas Wilm, Maxime Ulysse Garcia, Paolo Di Tommaso & Sven Nahnsen.
Nat Biotechnol. 2020 Feb 13. doi: 10.1038/s41587-020-0439-x.