Making various SNPs in a single track different colors

[Desiree Jacoby]

I would like to make certain SNPs certain colors associated with a function of our choosing. Below is the code I made for it, although any other description of the color it does not recognize it.

 

browser position chr4:90759047-90635020

track name=SNPs description="SNPs"

 

chr4 90758945 90758945 rs2301134

chr4 90759047 90759047 rs2619363

chr4 90759887 90759887 rs2619364

chr4 90760828 90760828 rs2583988

chr4 90678798 90678798 rs2572324

chr4 90721637 90721637 rs2583959

chr4 90678541 90678541 rs2736990 color=0,160,0

chr4 90711770 90711770 rs2737029

chr4 90674431 90674431 rs356168 color=240,0,0

chr4 90666041 90666041 rs356203

chr4 90675238 90675238 rs3857059

chr4 90655003 90655003 rs7684318

chr4 90734535 90734535 rs894278

chr4 90757505 90757505 rs1372520

chr4 90657491 90657491 rs3775423

chr4 90642464 90642464 rs356221

chr4 90646886 90646886 rs356165 color=93,51,129

chr4 90637010 90637010 rs356218

chr4 90637601 90637601 rs356219 color=93,51,129

chr4 90641340 90641340 rs356220

chr4 90635020 90635020 rs181489

chr4 90639515 90639515 rs11931074 color=240,0,0

chr4 90757394 90757394 rs3756063 color=0,0,255

chr4 90647278 90647278 rs17016074 color=240,0,0

[Cath Tyner]

Hello Desiree,

Thanks for contacting the UCSC Genome Browser support team. You can add color to your track as specified here:
http://genome.ucsc.edu/goldenPath/help/customTrack.html#MANAGE_CT
Note: search this page for "RGB" to see the examples of adding color to a BED9 in the section titled, "Track lines."

You will need to follow the file format for BED9, where the 9th column defines color:
http://genome.ucsc.edu/FAQ/FAQformat.html#format1

In your case, you will need to expand out to 9 columns to define a color for each item (but note you will need to put holder values in other fields, such as 0 for score, and matching coordinates in thickStart and thickEnd if you do not want your item to have different appearances of thickness).

For more details, please see this similar previously answered mailing list question:
https://groups.google.com/a/soe.ucsc.edu/d/msg/genome/xU_otQ4yClc/8TAb0zvxBQAJ

Example track line to try pasting in as a custom track:

browser position chr4:90759047-90635020
track name=SNPs description="SNPs" itemRgb=on

chr4 90678541 90678541 rs2736990 0 . 90678541 90678541 255,0,0
chr4 90674431 90674431 rs356168 0 . 90674431 90674431 255,0,0

Please respond to this list if you have further questions, and please always feel free to search our mailing list archives for related posts.

Thank you for contacting the UCSC Genome Browser support team. 

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​Enjoy,​

Cath
. . .

Cath Tyner

UCSC Genome Browser, Software QA & User Support

UC Santa Cruz Genomics Institute

UCSC Genome Browser

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