UCSC Genome Browser Custom Track Blank
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8 months ago
Daniel ▴ 30

Hello,

I have a bigwig (.bw) file which I can properly view on IGV. IGV makes it very difficult to edit the figure nicely so I am trying to view it in the UCSC genome browser. I uploaded my data to cyverse and used the custom track line here:

track type=bigWig name=“DMSO” color=255,255,255 visibility=2 bigDataUrl=https://data.cyverse.org/myDataURL/DMSO.bw

However, this successfully uploads but shows no shape/peaks. I believe some data is there though, because if I hover over the empty white-space, numbers appear around my cursor. Could anyone please tell me what I'm doing wrong? Sorry for my ignorance.

Thank you so much.

customtrack UCSC chipseq • 687 views
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wrong URL:

wget -O - https://data.cyverse.org/myDataURL/DMSO.bw 
(...)
Proxy request sent, awaiting response... 404 Not Found
2023-11-17 09:11:59 ERROR 404: Not Found.
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Hahaha sorry, I should have said the URL is fake (I can't share the data). But I can confirm it works, because when I copy/paste it into a browser the data can be downloaded. That same data then shows peaks on IGV.

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white is pretty unusual as a color for any plot. Is there a reason why you chose perfect white as the color for your track?

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21 days ago
brianlee ▴ 10

Here's an example bigWig track:

  1. Go to UCSC Genome Browser
  2. Select the Mouse mm9 assembly, or click this link: https://genome.ucsc.edu/cgi-bin/hgTracks?db=mm9
  3. Click the "My Data" menu and "Custom Tracks"
  4. Paste in the below (which points to a CyVerse hosted track):
track db=mm9 type=bigWig name=“CTCF” color=255,255,255 visibility=2 bigDataUrl=https://de.cyverse.org/anon-files/iplant/home/juanlmateo/CISSTEM/mm9/factors/CTCF.bigWig
  1. Click "Submit" and then on the next screen click "go to first annotation"
  2. As you describe there is an issue, the track is empty (white).

What is happening is the white color is making it hard to see the track. Change the color from your declaration of white to black.

  1. Repeat the above steps, but this time, add a new name and add the declaration of color=0,0,0 which will assign the track a black color.
track db=mm9 color=0,0,0 type=bigWig name=“CTCF_TEST_COLOR” visibility=2 bigDataUrl=https://de.cyverse.org/anon-files/iplant/home/juanlmateo/CISSTEM/mm9/factors/CTCF.bigWig
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