SRBrowse - An optimised genome browser for visualising and analysing methylome data at single-read resolution
We developed SRBrowse to derive additional information from next generation sequencing (NGS) methylome data. NGS data consists of short reads derived from genomes of the sample cells. While it is not possible to correlate the originating cells of individual reads, by analysing reads overlapping short regions (up to about half the average read length of the library), it is possible to ask questions regarding variation among cells of the sample population. We asked whether the CHH methylation signal in certain plant species is distributed evenly among cells, or whether there are distinct highly and lowly methylated reads, corresponding to cells with different methylation levels. Using this tool, we found different patterns of CHH methylation variation among cells correlated to the activity of CHH methylases CMT2 and DRM2. The results of this study are currently available as a preprint. The tool can be downloaded from GitHub and installed locally.
Preprint: https://www.biorxiv.org/content/10.1101/2020.03.05.974956v1
GitHub repository: https://github.com/zemachlab/srbrowse