This is a test version of Biostars. For the public version, visit https://www.biostars.org.
how to visualize methylation level in different gene structure.

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

next-gen r sequencing methylation bs-seq
• 3,620 views • link
updated by Antonio R. Franco Antonio R. Franco • written by xyhuang01 • xyhuang01

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

• 1 views • link
written by Devon Ryan Devon Ryan

2 answers

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

• 0 views • link
written by Antonio R. Franco 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

• 0 views • link
written by Antonio R. Franco Antonio R. Franco

Log in to answer this question.

More posts like this