[Genome] Genome-wide Map of custom track elements

[Benson, Craig C]

I have a custom track with about 90,000 elements of 10-bps long (known as CArG elements) in a bed format. I like how I can see the "density" map of my custom track for each chromosome, as illustrated in the attached screenshot for chromosome 1 of mm9. However, I was wondering if there was a way I can view this type of gene map for all chromosomes in one image? I have tried using the Genome Graphs program, but have had limited success. I also tried converting the bed to a "chromosome base" format with each CArG element assigned a value of 1, but it just showed a solid blue line above each chromosome. It would be most useful for me to be able to quickly look at all the chromosomes and see areas of increased CArG element density. Is there an easy way to create such an image or display? I have also attached the bed file for your reference.

Thanks!
Craig

Craig C. Benson, MD
Chief Resident of Internal Medicine-Pediatrics
University of Rochester Medical Center

[Brooke Rhead]

Hi Craig,

It sounds like you were on the right track: Genome Graphs is the tool we
have for displaying the entire genome at once. I am able to see your
data in Genome Graphs by doing the following:

- load the data as a custom track (which you have already done)
- go to the Genome Graphs tool (http://genome.ucsc.edu/cgi-bin/hgGenome)
and hit the "import" button
- select your custom track from the drop-down menus and give the data
set a name, if desired, then hit "submit"
- select your imported data from the "graph" menu for display

The image should update with a genome-wide view that shows the density
of the data. Does this work for you?

If you have further questions, please contact us again at
gen...@soe.ucsc.edu.

--
Brooke Rhead
UCSC Genome Bioinformatics Group

> _______________________________________________ Genome maillist -
> Gen...@soe.ucsc.edu
> https://lists.soe.ucsc.edu/mailman/listinfo/genome