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