ModRegion: Base Modification Results Tool

Background

• Epigenetics: DNA Methylation
• Nanopore DNA Sequencing
• Software tools to process raw nanopore sequencing data

Overview

During my time at Walter and Eliza Hall Institute of Medical Research, I developed a tool to quickly access, query and merge per-read base modification results from different software tools.

modRegion is primarily written to quickly extract regional methylation statistics from tsv outputted from methylation callers and it now supports: nanopolish, tombo and deepsignal

The motivation is that we are interested in fast querying output statistics over range of genomic positions at the single read resolution, and want to be able to have a common interface and coherent way of accessing the information as well as to save space on disk and on RAM.

modRegion allows users to extract, find overlaps of results with genes and plot per-read modification pattern over different regions.

Concretely, it has the following features:

• extract - pulls out statistics in the region(s) supplied from one or more base modification tsvs (uses lazy load and supports gzipped tsvs)
• overlap - finds statistics within ±overhang bases of genes
• plot - accepts filtered output and plots (using ggplot2)

Read more about the tool at https://github.com/yaeba/modRegion

Example output

Attaching here is an example plot output produced by modRegion given the methylation status of parental strain and maternal strain near an imprinting control region.