altColor and negateValues question

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Seth Goldman

Jun 23, 2021, 11:22:36 AMJun 23
UCSC Genome Bioinformatics Group,

I have a question about how the negateValues and altColor flags interact
when creating tracks by pasting track line information into Custom
Tracks section of the website.  I'm uploading bigwig files that contain
only positive values for both F and R strand data but I'd like to
display the R strands as negative.  Since the default altColor is
sometimes a little light, I'd like to apply a custom altColor.

I've tried these flags in the track line for my R strand bigwigs:

color=0,0,0 altColor=0,0,0 negateValues=on

but the negative values are displayed in grey, the default altColor,
rather than black which is what I had in mind.  Does negateValues
override custom altColor settings?  If so, is there a way to set a
custom altColor for negated values?



Seth Goldman, PhD
Nascent Transcriptomics Core, Director
240 Longwood Ave
HMS C-building, Room 204
Boston, MA 02115
PH: 617-432-1361

Jairo Navarro Gonzalez

Jun 24, 2021, 6:57:46 PMJun 24
to Seth Goldman, UCSC Genome Browser Discussion List


Thank you for using the UCSC Genome Browser and reporting your issues.

You have discovered a known issue when using the coloring options for bigWig custom tracks. If you
set altColor (or color) to 0,0,0 then the Genome Browser code believes that the color is unspecified.
The current workaround is to set altColor to 1,0,0 instead of 0,0,0 to use the black color. For example,

browser position chr12:56,707,300-56,707,399
track type=bigWig name="my negative strand" color=1,0,0 altColor=1,0,0 negateValues=on bigDataUrl=

I hope this is helpful. If you have any further questions, please reply to
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

Jairo Navarro
UCSC Genome Browser

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Seth Goldman

Jun 25, 2021, 4:19:12 PMJun 25
to Jairo Navarro Gonzalez, UCSC Genome Browser Discussion List

Thanks for getting back to me.  I've noticed that the problem is not restricted to black.  For example, if I specify
color=150,0,0 altColor=150,0,0 negateValues=on
the track ends up pink instead of dark red.

I'm also having trouble getting the work-around for black to perform as expected.  I tried
color=1,0,0 altColor=1,0,0 negateValues=on
but the result is still gray for me.  Is there another setting I should

To explore a bit more, I tried setting the altColor to a different hue than the color.  If I try
color=150,0,0 altColor=1,1,150 negateValues=on
The result is blue, not red but the blue shade is not 1,1,150 (dark blue) but a lighter shade: 141,142,203 by my computer's color meter.

It seems like negateValues lightens the custom altColor instead of using it unmodified.  That is, it appears to be making an altColor of the altColor.  Does that sound plausible?  Is there a workaround?


Seth Goldman, Ph.D.
Nascent Transcriptomics Core, Director
Harvard Medical School
240 Longwood Ave
C-Building, Room 204
Boston, MA 02115
Phone:  617-432-1361

Matthew Speir

Jul 2, 2021, 6:25:58 PMJul 2
to Seth Goldman, Jairo Navarro Gonzalez, UCSC Genome Browser Discussion List
Hi, Seth.

We're having issues replicating the issues you are describing in regards to the altColor setting. Is it possible for you to share a link to a session that demonstrates the issues you are seeing? If this session contains private data, you may instead share it with our private mailing list,

Thank you!

Matthew Speir

UCSC Cell Browser, Quality Assurance and Data Wrangler

Human Cell Atlas, User Experience Researcher

UCSC Genome Browser, User Support

UC Santa Cruz Genomics Institute

Revealing life’s code.

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