Visualizing human genomic loci

Question

[James]

Hi everyone, I want to be able to generate a genomic loci figure that looks like below, where I can mark loci of interest over the entire genome (I got the figure from this paper: https://www.nature.com/articles/s41598-022-15058-0)

Would you have any recommendation on where / how I could prepare the figure like this? I have some experience using UCSC genome browser, but the output I get from it is not as neat as this figure. Thank you.

edit: I have checked out Artemis, ggbio, genVisR, genoverse, and a couple other tools I found from this forum, but none of them seemed like exactly what I needed. Thanks again!

[Yogi]

Did you double check that they don't discuss the software used in the "Methods section"?

[James]

Hi Yogi, Yes, I have read the methods section and there was no particular mentioning of the software that was used to create the figure. I think I have some good leads now. Thanks!

Answer 1

[Michael]

There are a lot of tools to plot chromosome ideograms with data and there are a lot of posts here:

• Drawing Chromosome Ideograms With Data
• Ideogram.js: a JavaScript library for chromosome visualization
• Drawing yeast chromosome ideograms with data

(Some of the links found above might not work anymore)

RIdeogram: https://cran.r-project.org/web/packages/RIdeogram/vignettes/RIdeogram.html

Gviz: https://www.bioconductor.org/packages/devel/bioc/html/Gviz.html

karyotypeR: https://bernatgel.github.io/karyoploter_tutorial/

[James]

Hi Michael, thank you very much for your comment with lots of great information!

Answer 2

[brianlee]

The UCSC Genome Browser does have a "Genome Graphs" tool: https://genome.ucsc.edu/cgi-bin/hgGenome

It is accessible under the top "Tools" menu, 3rd from the bottom. The tool is a little old, and uses a different kind of format. here is the help page on the tool: https://genome.ucsc.edu/goldenPath/help/hgGenomeHelp.html

The lines can be like this in the data:

chrX 100000 1.23

or

rs10218492 0.384 0.882

Likely most will want the chromosome base format, e.g., chr1 130000 (Note that the first base in a chromosome is considered position 0) followed by a numerical marker for height.

There is also an " Importing data" feature that lets you convert existing tracks, or your attached custom tracks.

Here are step-by-step examples.

1. Go to the tool
2. Click the "upload" button (note the import button too)
3. Here you could upload a file, or paste some values. Paste the below:

chr2 100100000 2.3 
chr2 100100500 4.5 
chr2 100101000 1.2

1. Click submit, then OK, with the message that "3 markers" have been read.
2. Now, when you return the "graph" has the defaulto of "--nothing--" you have to change that from "--nothing--" to "User Track 1"
3. Note the below image now has a small spike on chr2.

You can search the Browser mailing list archives for more examples and details: https://groups.google.com/a/soe.ucsc.edu/g/genome/search?q=hgGenome