Visualizing 450 K Methylation Array Data In Igv

Question

[kanwarjag]

I have a 450 K infinum DNA methylation array data with methylation b values. I would like to plot it in any genome browser prefer is IGV. I can convert generate coordinates bed file and then upload to genome browser- IGV/ UCSC. My question is can I vary the histogram as per level of beta values? Is there any other nice way of visualizing 450 methylation data in genome browser?

Thanks

Answer 1

[dario.garvan]

BED format is not the right format. You need to output the data in bedGraph format.

[Jorge Amigo]

I also agree that bedgraph is the format that would be more helpful for your interests. you can define start and end chromosome positions, plus a value that usually represents coverage, but that you can use it to represent the methylation b values instead. you can still gzip the file, and IGV will still be able to deal with it. a similar approach (reducing file size to improve data storage and make data access faster) would be to transform that bedgraph file to bigwig format using UCSC's bedGraphToBigWig (find it here), which is an indexed binary format that works great on IGV. plus you can apply colors to this track on IGV depending on thresholds, which is useful to detect high and low peaks for instance.

Answer 2

[Charles Warden]

COHCAP (using the "Average per Site" workflow) will create .wig files for 450k methylation values (per site, per group as well as for delta-beta values, if you are comparing two groups), which can be visualized using IGV, UCSC, etc.

Outside of the genome browser, COHCAP can also create box-plots and correlation plots, if you have paired gene expression data (using the "Average per Island" workflow).

http://nar.oxfordjournals.org/content/41/11/e117.long

http://sourceforge.net/projects/cohcap/

I think this is a pretty good strategy, but of course I am biased ;)