Visualizing Chip-Seq And Bis-Seq (Dna Methylation) Data

Question

[Ali]

I want to generate a journal picture similar to the following, visualizing both chip-seq and bisulfite-seq data:

(from C.A.Gifford et.al., Cell 2013),

Here bisulfite-seq data are represented as points in the first row and Chip-seq data are visualized in next rows.

Do you know any software that can generate similar pictures in journal quality (vector type image, beautiful graphics)? I want the bisulfite-seq data to be represented in the same way as picture above.

Answer 1

[Istvan Albert]

In general very pretty plots in papers are the results of long and tedious, often manually intensive processes. There is no tool that will just do this exactly with minimal effort.

Use any plotting approach that you already know and keep tweaking it until you get what you want.

This appears to be a multiplot with six horizontal regions, where the x scales, x-axis and x-tickmarks are hidden

[Ali]

Thanks Istvan. I have seen some functionalities in a software like "igv". Chip-seq data are visualized fairly similar to what I need. I am not sure if it can represent methylation data as good as the above picture or not. Do you have any idea?

Answer 2

[Steve Lianoglou]

The Gviz bioconductor package will get you pretty close to a (very) pretty picture.

Skim through the Gviz user's guide to get an idea of some of the things it can do for you.

Answer 3

[Ali]

I could generate a similar visualization using the integrated genome viewer (IGV) by Broad Institute. We can simply right click on any row (chip-seq or bis-seq data representation) and select type of graph among points (the first row of picture below), barplot (the second row), line plot or heatmap, or even change the color or height of the chart.

It's really a nice utility that produces excellent pictures with minimal effort.

Answer 4

[shenli.sam]

Have you calculated coverage for your bisulfite-seq data? If yes, IGV can certainly draw a plot like that.

If you want global visualization for your ChIP-seq at functional genomic regions, consider ngs.plot. It generate beautiful figures in vector-based format, which can be loaded into an image editor for further furnishing.