Wednesday, October 9, 2013

v25: new display methods for methylC-seq and RRBS experiments

Version 25 features a nice way to display CpG methylation data, and the track background color configuration.


CpG methylation track
Tracks like those generated by methylC-seq (bisulfite sequencing), and Reduced Representation Bisulfite sequencing (RRBS) assays are single-base resolution. There won't be any data unless there's a CpG site. Traditionally such tracks are displayed as numerical track with a number ranging from 0-1 for all bases. That leads to a confusion of "0 value (no methylation)" and "lack of data (not a CpG)".

Now a new display method is available to address this issue:




This example shows two methylC-seq tracks in human hg19. Methylation levels over CpG sites are marked out by red/blue bars, and the "counter-value" is marked out with gray. A long gray bar means the CpG site has very low methylation level. This way you can tell a unmethylated CpG site from those blank regions with no CpG sites.

This rendering method is suitable for numerical data with incomplete coverage of the entire genome. In the other words, if your track hasn't got a value for every bp in the genome, you should use this display method.

To use this display method, convert your track into bedGraph format.

To turn on the effect, add this attribute in the track object in the datahub:

barplot_bg:"#cccccc",

Or in the embedding code, add this:

barplotbackground:"#cccccc",




Track background
Now it's possible to apply background color to tracks. Simply check the "use background color" option in Configure menu:



To apply background color in datahub or embedded browser, add this in track object:

backgroundcolor:"#cccccc",