Custom track error in Table browser

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Umashankar Singh

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Nov 2, 2021, 11:56:42 AM11/2/21
to gen...@soe.ucsc.edu, genom...@soe.ucsc.edu
Hi,
I am trying to load two custom tracks. However, the table browser returns only one; it automatically overwrites the last uploaded bedgraph file with the latest one. Even if I try using http links from Cyverse, the problem remains. From two links, one for each bw file, it still returns just one custom track. Please help. Thanks very much.
PS: links are as follows:


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Best regards
---
Umashankar Singh, Ph. D.
Associate Professor
HoMeCell Lab, Biological Engineering
Indian Institute of Technology
Gandhinagar, Gujarat
India.

Ph (O): +91-79 23 95 24 80

Brian Lee

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Nov 2, 2021, 6:57:23 PM11/2/21
to Umashankar Singh, UCSC Genome Browser Mailing List, genome-www list

Dear Dr. Singh,

Thank you for your question about custom tracks in the Table Browser.

For one item, I noticed you have CyVerse links, I wanted to share on the first Tuesday of each month they have site maintenance (https://cyverse.org/maintenance: November 2, 2021 / December 7, 2021 / January 4, 2022). This could explain any CyVerse connection issues you experience today.

For the Browser, when uploading or connecting to a custom track, the software attempts to decipher what type of data is being added and if no track name is assigned it will name the track "User Data." If you don't specify a name and add a second track, the "User Data" name will be applied again and will overwrite the first data.

Here is an example, try pasting this data in the Custom Track Page:

chr19 49302000 49302300 -1.0
chr19 49302300 49302600 -0.75
chr19 49302600 49302900 -0.50
chr19 49302900 49303200 -0.25

It will result in a track where the Browser will automatically assign track name='User Track' description='User Supplied Track'.

If you then add a second track on the custom track page, such as the below,

chr19 49303200 49303500 0.0
chr19 49303500 49303800 0.25
chr19 49303800 49304100 0.50

The new data will display, but the previous track name='User Track' description='User Supplied Track' track will be overwritten.

One solution is to add a track line, see more about track lines here:
http://genome.ucsc.edu/goldenPath/help/customTrack.html#TRACK

If you return to the custom track page and try uploading these two tracks you will see they are separate now (you can even add both in one cut and paste):

track name='track one' description='This is my first track showing X'
chr19 49302000 49302300 -1.0
chr19 49302300 49302600 -0.75
chr19 49302600 49302900 -0.50
chr19 49302900 49303200 -0.25

track name='track two' description='This is my second track showing Y'
chr19 49303200 49303500 0.0
chr19 49303500 49303800 0.25
chr19 49303800 49304100 0.50

The most important item is to note that you give separate names to each track.

You also shared bigWig links to CyVerse (fileName.bw). Those should work and give separate names to each track. The software will automatically assign a track line to the files where the name is generated from the file name, and as long are the file names are different both will load.

Here are examples, using the hgct_customText= parameter to attach 2 custom tracks (with similar names, but each is different):

https://genome.ucsc.edu/cgi-bin/hgTracks?db=hg19&hgct_customText=http://genome.ucsc.edu/goldenPath/help/examples/bigWigExample.bw
https://genome.ucsc.edu/cgi-bin/hgTracks?db=hg19&hgct_customText=http://genome.ucsc.edu/goldenPath/help/examples/bigWigExample2.bw

Click both links and a track name=bigWigExample.bw and a track name=bigWigExample2.bw will be created.

Now go to the Table Browser, for instance using the top Tools menu. You can then set the "group: Custom Tracks" and you will see you can select "track: bigWigExample.bw" or "track:bigWigExample2.bw". If we wanted to load this tracks with names other than the file name, we could give track lines to the browser, as demonstrated above, but where a bigDataUrl= parameter would point to the URL of the bigWig online. When getting output from the Table Browser, be sure to set the "region: genome" in case the position you are currently viewing has no data.

Thank you again for your inquiry and for using the UCSC Genome Browser. If you have any further public questions, please send new questions to gen...@soe.ucsc.edu. All messages sent to that address are archived on a publicly accessible forum to help others find answers to similar questions. If your question includes sensitive data, you may send it instead to genom...@soe.ucsc.edu, which is a private internal list to our support team.

All the best,

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