Epigenomics is the study of genome-wide distributions of chromatin modifications. Our knowledge of epigenomics has drastically improved with next-generation sequencing (NGS) with techniques like whole-genome bisulfite sequencing (WGBS) and chromatin immunoprecipation sequencing (ChIP-seq). With the large quantities of data being produced, data visualization is an important step for quality control and exploration.
Numerous software programs exist to visualize genomics data; most popular is the genome browser. These existing programs focus on a limited subset of data types such as mRNA-seq and single-nucleotide polymorphisms. Beyond ChIP-seq, there is very little support for visualizing epigenomics.
I have developed additional tools, plugins, for the genome browser JBrowse that support epigenomics data. Specifically, I have created ways to view context-dependent DNA methylation from WGBS. The methylation context is very important to its function, particularly the combination of contexts in a region. Traditional genome browsers require the DNA methylation contexts as separate “tracks” which makes it extremely difficult to see combinations and patterns. The methylation plugin I have developed allows for all methylation contexts to be displayed on one track with the context differentiate by color.
Small RNA are also important in epigenetics as they can regulate gene expression and impact DNA methylation. Traditional browsers support small RNA-sequencing data but are missing features specifically useful for small RNA-seq. Specifically, the size of a small RNA is indicative of function. I have developed a small RNA-plugin for JBrowse which colors reads based on size and improves visualization by separating reads from the plus and minus strand.
Finally, ChIP-seq and similar techniques such as ATAC-seq, DNaseI-seq, Mnase-seq, are supported in JBrowse. However, it is missing features that are useful specifically in epigenomics. For example, in ATAC-seq, it is beneficial to know strand-specific coverage (not currently support by JBrowse). I have created a plugin that easily supports these strand-specific coverage tracks. This plugin is also very useful for coverage views of mRNA-seq and smRNA-seq.
In addition to the epigenomics plugins, I have also created a plugin which makes taking browser screenshots easier and with customized view options. This plugin leverages PhantomJS Cloud to do the screenshot and is able to output images in PNG, JPG, and PDF. The screenshot plugin is particularly useful for scientific data communication.