how to visualize methylation level in different gene structure.

Question

[xyhuang01]

Dear All,

I would like to know how to make the figures like below to show the methylation level at genes or TEs, and their 1-kb upstream and downstream regions at the sequence context of CG, CHG, and CHH. Now I already have the whole genome methylome by BS-seq. Is there any tools to make the figures? or where can i find the sample script (in R or Linux) to do that?

Thanks!

[Devon Ryan]

Those are similar to what plotProfile in deepTools does, though I've never tried that with methylation data.

[natasha.sernova]

There are a few tools:

Epigenie:

http://epigenie.com/epigenetic-tools-and-databases/

methyAnalysis: an R package for DNA methylation data analysis and visualization

http://www.bioconductor.org/packages/3.3/bioc/vignettes/methyAnalysis/inst/doc/methyAnalysis.pdf

MethylSig: a whole genome DNA methylation analysis pipeline

http://bioinformatics.oxfordjournals.org/content/30/17/2414.full

I've never used them.

Answer 1

[Antonio R. Franco]

If you are interested in CHH and CHG, then you must be working with plant genomes Be aware that most of programs analyzing methylomes, are designed to use CpG methylation only

Answer 2

[Antonio R. Franco]

Take a look to this video tutorial about how to manage methylation with IGB. Is not exactly what you are asking, but at least it will be useful