This project is part of my MSc Bioinformatics project in undertanding DNA methylation patterns in mammalian cells using OXford Nanopore sequensing data. It explores whether methylation patterns differ significantly between wild-type and mutant mammalian cells lacking key DNA methyltransferases. The pipeline is built around the DSS package in R to:
- Detect differentially methylated loci (DMLs) and regions (DMRs)
- Filter for canonical chromosomes
- Evaluate biological relevance and statistical significance of findings
The motivation behind this work is to better understand how gene body methylation may influence gene expression. Long read sequencing offers a promising way to observe these patterns at high resolution across the entire genome. Through this project so far, I gained experience working with large methylation datasets, developing shell workflows, and performing statistical analyses using R.
Clone the repository:
git clone https://github.com/cemileblks/dss-analysis.git
cd dss-analysis
Install required software:
- R (v4.0+)
- R packages:
DSS,bsseq,GenomicRanges,rtracklayer - Command-line tools:
bedtools,awk,bash - IGV or UCSC Genome Browser (for visualisations)
This pipeline processes .bedMethyl and .bedGraph files generated from Oxford Nanopore methylation data. It performs differential methylation analysis using the DSS R package and produces .bed and .bw files for downstream visualisation and analysis.
The outputs include:
- Lists of differentially methylated loci (DMLs) and regions (DMRs)
- Filtered and converted
.bedfiles for genome browser tracks - A
.bigWigfile showing methylation differences between conditions - (In progress) A statistical summary of significant DMLs/DMRs in
.Rmdformat
-
DSS R package documentation
Used for differential methylation analysis in R. -
CLASS 2023 tutorials
Helpful for understanding genomic overlaps and usingGenomicRanges.
Special thanks to my MSc supervisor and lab group for their guidance through this project.
This project is shared for academic and educational purposes only and does not currently use a formal open-source license. If you plan to reuse or modify the code, please cite the project appropriately.