Highlighting Feature in UCSC

[Johannes C. Hellmuth]

Hi there,

in the UCSC Genome Browser Public Support forum 'Highlighting Feature in UCSC’ Cath Tyner offer help on a scripting method to translate a custom track into a highlight URL. That would indeed be very helpful.

On the points raised in that forum:

- different highlight colors would be great

- regions do not overlap

- I have a bed custom track that I wish to highlight

Other than that, our track hubs are set up pretty standard.

Thanks,

Johannes 

Johannes C. Hellmuth, M.D.

Postdoctoral Associate in Medicine

Melnick Lab

Weill Cornell Medicine

Division of Hematology & Medical Oncology
413 E 69th Street, Room BB-1462
New York, NY 10021

T 646-962-6726

[Jairo Navarro Gonzalez]

Hello Johannes,

Thank you for using the UCSC Genome Browser and your inquiry.

Could you clarify what you are trying to accomplish with these highlights? Do you have regions defined inside a custom track that you would like highlighted in the genome browser? Unfortunately, we do not have a way to use a custom track as the source of highlighting regions and colors at the moment but is in our work queue. If you would like email updates about the UCSC Genome Browser, you can subscribe to our Announcements List:

• Subscribe: Email genome-annou...@soe.ucsc.edu
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There is a workaround to pass highlight regions through the URL and the color is defined using hex codes. You could highlight these regions using the URL parameter on the following page:

highlight=<DB>.<CHROM>:<START>-<END>#<COLOR>|...

- highlight one or more regions in a given color on the image.

Note that the arguments have to be URL-encoded for Internet browsers,
so ":" becomes "%3A", "#" becomes "%23" and "|" becomes "%7C".

- example link to highlight two parts of the ABO locus in red and blue.

Combining this highlight= parameter with the hubUrl=, you can load your hub with highlights. For example, you can use the following URL to load a hub and defines highlight regions for hg19:

http://genome.ucsc.edu/cgi-bin/hgTracks?db=hg19&position=chr21%3A33031597-33041570&hubUrl=http://vizhub.wustl.edu/VizHub/RoadmapRelease3.txt&highlight=hg19.chr21%3A33032920-33033566%23AA0000%7Chg19.chr21%3A33036057-33036679%23FF5733%7Chg19.chr21%3A33038320-33038811%23F3F339

A more complex alternative to add these highlights within a given region is to edit your cart. The "cart" is a hidden table that contains the persistent selections that users have made in the Genome Browser. You can do this by going to http://genome.ucsc.edu/cgi-bin/cartDump and then click the Show as updatable table option to modify your cart's contents. Once you can edit your cart, search for "highlight", and you should see a list of text highlights separated by "|" pipes, i.e.

 hg38.chr1:11161768-11161768#aaedff | hg38.chr1:11161739-11161739#aaedff 

You can add your highlights by modifying that field, clicking the refresh button at the top page, and then navigate back to the main Genome Browser page, http://genome.ucsc.edu/cgi-bin/hgTracks. To keep these highlights from being deleted, save your settings inside of a session.

I hope this is helpful. If you have any further questions, please reply to gen...@soe.ucsc.edu.
All messages sent to that address are archived on a publicly-accessible Google Groups forum.
If your question includes sensitive data, you may send it instead to genom...@soe.ucsc.edu.

Jairo Navarro 
UCSC Genomics Institute

Want to share the Browser with colleagues?
Host a workshop: http://bit.ly/ucscTraining

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