Which Genome Browser Can Get This Image

Question

[liqingyan]

Hello

Can anybody know which genome browser can show peak image like Figure a as below.

Answer 1

[seidel]

The UCSC genome browser can do that. You can configure the image to not show the default blue lines, and set the scale to display the peaks like in your figure, and then you can export the image as pdf, so you can mark it up further if you like The image in your example has had various attributes added manually, using an editor (i.e Adobe Illustrator, or your favorite alternative).

[Mary]

I think I remember that paper, too--although it's not cited--and it's also possible it's back one assembly to reproduce this most closely. To locate the specific tracks that are named you may have to go to Mar 2006 at UCSC. Some stuff got renamed and reorganized on the next assembly.

Answer 2

[David Langenberger]

The images under a) are for sure UCS pictures, pimped with Adobe Illustrator, as Seidel already mentioned.

And I think for b) they used a tool called sitepro from the CEAS package. It draws the average signal (from a WIG) in a given list of sites of interest (from a BED).

Answer 3

[dariober]

You can get pretty close with R/Bioconductor Gviz, this is the vignettes

Answer 4

[Neilfws]

The glyph for the NANOG gene looks a lot like IGV.

As seidel said, the image has had quite a lot of extra "manual" work done to it. There are several browsers - particularly UCSC and IGV - that could be used to generate something like the figure, if not the exact result.

Answer 5

[QVINTVS_FABIVS_MAXIMVS]

Those look like R/MatLab figures. You can import your bedgraph file into R and use the genome position and the data in your bedgraph column to plot the data.

The pie chart was made in Microsoft Office suite

You can get similar looking figures in UCSC genome browser and IGV. But if you want figures that look exactly like those, you need R or MatLab