Highlighting Feature in UCSC
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Branch, Justin
Mar 23, 2017, 1:53:36 PM3/23/17
to gen...@soe.ucsc.edu
Hi There,
I want to highlight my SNVs by color that makes it way down the entire Genome Browser Window. Similar to what you guys have shown here
How can I accomplish this?
Justin Branch
SMART PREP Program
Baylor College of Medicine
Lab of: Dr. Rui Chen
Rm: T836
Cath Tyner
Mar 24, 2017, 7:51:21 PM3/24/17
to Branch, Justin, gen...@soe.ucsc.edu
Hello Justin,
Thanks for posting your highlighting question to the UCSC Genome Browser support forum! Below I've included more information about highlighting tracks in the browser window.
1. As you may already know, you can create highlights within your browser window by following the steps described in our tracks help page, at the "Highlighting a region" section
2. Please note our "Optional parameters in URLs" help section
See also: https://genome.ucsc.edu/FAQ/FAQlink.html
You can edit the color of your highlights by editing the hex color code found within the url. In the example you provided, I see the red and blue color codes:
0000FF and AA0000.
Below is an example where the blue hex code has been changed to red:
https://genome.ucsc.edu/cgi-bin/hgTracks?db=hg19&position=chr9%3A136136597-136139844&highlight=hg19.chr9%3A136138630-136139650%23AA0000%7Chg19.chr9%3A136136630-136137650%23AA0000
The above steps may provide a solution for you. However, please
We do not have a way to use a custom track as the source of highlighting regions and colors, but we might be able to suggest a simple scripting method to translate a custom track file into a highlight URL or multi-region file. To best assist you, please let us know:
* Unsubscribe: Email genome-announce+unsubscribe@soe.ucsc.edu
Thanks for posting your highlighting question to the UCSC Genome Browser support forum! Below I've included more information about highlighting tracks in the browser window.
1. As you may already know, you can create highlights within your browser window by following the steps described in our tracks help page, at the "Highlighting a region" section
.
2. Please note our "Optional parameters in URLs" help section
, specifically - S
tep 2, the "highlight" bullet point.
See also: https://genome.ucsc.edu/FAQ/FAQlink.html
You can edit the color of your highlights by editing the hex color code found within the url. In the example you provided, I see the red and blue color codes:
0000FF and AA0000.
Below is an example where the blue hex code has been changed to red:
https://genome.ucsc.edu/cgi-bin/hgTracks?db=hg19&position=chr9%3A136136597-136139844&highlight=hg19.chr9%3A136138630-136139650%23AA0000%7Chg19.chr9%3A136136630-136137650%23AA0000
The above steps may provide a solution for you. However, please
respond to the support forum and
provide answers to the following questions if you need further assistance:We do not have a way to use a custom track as the source of highlighting regions and colors, but we might be able to suggest a simple scripting method to translate a custom track file into a highlight URL or multi-region file. To best assist you, please let us know:
- Do you need to use different colors, or is mono-color good enough?
- Do any of your regions overlap?
- Do you have a BED custom track file already, or some other file format?
Thank you again for your inquiry and for using the UCSC Genome Browser.
Please send new and follow-up questions to one of our UCSC Genome Browser mailing lists below:
* Confidential/private help: Email
genom...@soe.ucsc.eduUCSC Genome Browser Announcements List (email alerts for new data & software):
* Subscribe: Email genome-announce+subscribe@soe.ucsc.edu * Unsubscribe: Email genome-announce+unsubscribe@soe.ucsc.edu
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