Question: how to visualize methylation level in different gene structure.
1
gravatar for xyhuang01
2.9 years ago by
xyhuang0110
xyhuang0110 wrote:

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!

CG, CHG, and CHH methylation level at genes (A), TEs (B), and their 1-kb upstream and downstream regions

ADD COMMENTlink modified 2.8 years ago by Antonio R. Franco4.0k • written 2.9 years ago by xyhuang0110

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

ADD REPLYlink written 2.9 years ago by Devon Ryan88k

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.

ADD REPLYlink modified 2.8 years ago • written 2.8 years ago by natasha.sernova3.4k
0
gravatar for Antonio R. Franco
2.8 years ago by
Spain. Universidad de Córdoba
Antonio R. Franco4.0k wrote:

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

ADD COMMENTlink modified 2.8 years ago • written 2.8 years ago by Antonio R. Franco4.0k
0
gravatar for Antonio R. Franco
2.8 years ago by
Spain. Universidad de Córdoba
Antonio R. Franco4.0k wrote:

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

ADD COMMENTlink modified 2.8 years ago • written 2.8 years ago by Antonio R. Franco4.0k
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