Long-read methylation data analysis with NanoMethViz and Bioconductor
In this workshop, we provide a Bioconductor analysis pipeline for DNA methylation. We highlight NanoMethViz, an R package for the analysis of DNA methylation using long-read sequencing data. DNA methylation is a critical epigenetic mechanism involving the addition of methyl groups to DNA, affecting gene expression without altering the genetic sequence. This process plays a pivotal role in development, health, and disease, making its study essential. Starting from modBAM files, which are currently the standard output of ONT-based modification calling pipelines, we will learn to perform exploratory data analysis to uncover high level methylation patterns over genes and across samples. We proceed to delve deeper to find differential methylated regions (DMRs), and associate them with genes to potentially uncover features that are affected by epigenetic regulation. Using NanoMethViz we can plot the methylation signals in the discovered DMRs or other regions of interest in order to generate a high resolution plots of methylation profiles, as well as data from individual long-reads. We will also cover data querying features of NanoMethViz to perform more custom analyses on the raw data, as well as more advanced features of the package for methylation data analysis.