BigWig tracks : color change

[Katerina Hatzi]

Hi, 

Thanks a lot for providing us with such a powerful tool as UCSC. We recently switched to displaying BigWig tracks and I am wondering if there is a way we could change colors on these tracks through UCSC. 

I realize we can go back to the wig files, change  color and convert back to bigwig but we are really missing a way to directly do this on the browser, while other track settings can be easily modified. 

Please let me know if that would be possible. 

Thanks a lot,

Katerina 

[Cath Tyner]

Hi Katerina,

Thanks for contacting the UCSC Genome Browser support team. Can you clarify how you are displaying bigWigs? 

Are you:

* displaying native tracks that live in the UCSC Genome Browser,

* displaying custom tracks, 

* displaying custom tracks in a hub,

* using a mirror installation via GBiB, or

* using a mirror installation via GBiC script or manual installation?

Cath
. . .

Cath Tyner

UCSC Genome Browser, Software QA & User Support

UC Santa Cruz Genomics Institute

UCSC Genome Browser

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[Katerina Hatzi]

Thanks for your prompt response. We are currently using a hub (ftp server) to see our bigWigs so number 3 of your list.

I actually did not think there is a way to upload them as native tracks that live in UCSC. 

[Cath Tyner]

Hello Katerina,

>I actually did not think there is a way to upload them as native tracks that live in UCSC

Regarding #1 on the list, I was just wondering if you were displaying some of our bigWig native tracks that reside in the browser (sounds like you are not). ​Correct, there is no way to do this. Native tracks are hosted here at UCSC and are distinct from custom tracks/hubs.

Regarding your question about being able to customize track colors from the browser's user interface, this is currently a feature which has not yet been implemented. However, there has been some recent internal discussion about adding this feature, as we think it would be a valuable tool for our users. If we do implement this feature in the future, we would likely announce it through our announcements list and news page.  I will also make a note to contact you directly if/when this feature is released. 

Until then, below are coloring options:

First, I recommend removing the color definition line from your wiggle file/s, and then go ahead and convert to bigWig, without a color line. This way, you'll be able to set the coloring within trackDb. 

You can control coloring (see "color" and "altColor") via trackDB settings:

http://genome.ucsc.edu/goldenPath/help/trackDb/trackDbHub.html

For examples and specifications for composite and overlay views/track groups, see these sections:

* http://genome.ucsc.edu/goldenPath/help/trackDb/trackDbHub.html#compositeTrack

* http://genome.ucsc.edu/goldenPath/help/trackDb/trackDbHub.html#aggregate

Note that by default, the Browser re-loads hub files every five minutes, so you would have to wait until the file re-loads to see your changed . When editing hub.txt, genomes.txt, and trackDb.txt, you can shorten this delay by adding udcTimeout=1 to your URL. For more information, see the Debugging and Updating Track Hubs section of the Track Hub User Guide.

For additional reference, below is a method to change colors for custom tracks only (not track hubs) via browser interface:

1. Go to My Data > Custom Tracks

2. I'll use a basic bigWig custom track example, which you can paste in:

track type=bigWig name="Example One" description="A bigWig file" bigDataUrl=http://genome.ucsc.edu/goldenPath/help/examples/bigWigExample.bw

3. You can go to the browser to see that the bigWig is the default black color.

4. Now, click on the track shortLabel, or click on the vertical gray left-side button in the browser track and then click the button "Update custom track"

Or, you can click on My Data > Custom Tracks and then click on the link for your track to get to the "update custom track" page.

5. Edit the configuration to add a color definition line such as:

track type=bigWig name="Example One" description="A bigWig file" color=15,94,94 bigDataUrl=http://genome.ucsc.edu/goldenPath/help/examples/bigWigExample.bw

6. You can now go back to the browser and see that the bigWig is now colored green/blue.

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

[Cath Tyner]

Hi again Katerina,

I'd like to clarify part of my response:

You should not need to regenerate your bigWig files; there is nothing within the wiggle file itself that specifies color. Only the 'track' definition line would be defining the color, or the trackDb.txt entries for a track hub. You should only need to alter the metadata for your custom tracks or hub,  as specified in my last response. 

If instead you are using a bigBed file with a column nine 'itemRgb' definition, you would need to rebuild your bed file, or use other types of coloring options that are not 'itemRgb' for bigBed files. Please respond if you would like more information about coloring bigBed files. 

Cath
. . .

Cath Tyner

UCSC Genome Browser, Software QA & User Support

UC Santa Cruz Genomics Institute

UCSC Genome Browser