Methylation tracks

[alexharkess]

I have been toying around with how to make tracks that show methylation in CpG, CHG, and CHH sequence contexts. The annoj browser does it very well (http://neomorph.salk.edu/epigenome/epigenome.html), letting you select which sequence context you want to display, and it displays both strands on the same track.

I understand that there are a few issues implementing something like this into jbrowse. The first being there's currently no way in jbrowse to display information from both strands at once, since most formats don't let you have multiple Y values (ie., one positive and one negative) for a given X coordinate.

I think we could solve part of this problem by implementing combination tracks. For instance, if jbrowse could automatically generate tracks for CpG, CHG, and CHH sites on the reference, I could make a combination track using a bigwig file containing plus/minus strand combined methylation at every C site in the genome. I imagine auto-producing three checkboxes on my tracklist, letting me pick which sequence context I want to display as a combination track.

Best,
Alex

[colindaven]

Interesting idea. From the Bismark bedgraph output I can generate a bigwig file for either all CpG sites (default) or all Cs in the genome. I will attempt to manually split the C's into the three possible contexts and upload them as three different tracks.

This functionality would be quite difficult to implement into JBrowse however, I bet the IGV developers put a lot of time and effort into their nice implementation of coloring and sorting by BAM tags.

[cmdcolin]

@bhofmei has made some great jbrowse plugins in this area https://github.com/bhofmei/jbplugin-methylation https://github.com/bhofmei/jbplugin-nucdens