UCSC genome browser custom track
Emma Dolan
Hi genome team,
I’ve encountered a “Couldn’t open” error in my attempt to upload a bigWig file to a custom track in the genome browser, so I’m hoping someone can help me through it. I’m in the Add Custom Tracks page, and I’ve typed the following into the first box.
track name="6hr Veh 1"
track type=bigWig bigDataUrl=https://usegalaxy.org/api/datasets/f9cad7b01a47213550329ab30779cd1d/display?to_ext=bigwig
The Url links to my workspace in Galaxy, where my bigWig files are saved. When I click Submit, the genome browser gives me the following warning:
Warning
Couldn't open https://usegalaxy.org/api/datasets/f9cad7b01a47213550329ab30779cd1d/display?to_ext=bigwig
Is this an issue with the genome browser? Or maybe a permission issue within Galaxy? Is there another recommended way to upload bigWig files into custom tracks? I’m open to all suggestions!
Thanks,
Emma Dolan
Luis Nassar
Hello, Emma.
Thank you for your interest in the Genome Browser.
Unfortunately in order to display remotely hosted files (such as big* formats like bigWig or bigBed), the server needs to support byte-range requests. What that means is that the Genome Browser can request only a small part of the file, say only the 100bp in a range like chr1 1-100, without having to read/download the whole file.
The following page explains the topic further and provides some hosting options (http://genome.ucsc.edu/goldenPath/help/hgTrackHubHelp#Hosting). Galaxy does not support these requests, but many of our users find success with CyVerse and github (which is great for small <100Mb files). We also see that you are writing in from a .edu address. Many universities provide hosting space, so that may also be another solution for you.
I hope this is helpful. Please include gen...@soe.ucsc.edu in any replies to ensure visibility by the team. All messages sent to that address are archived on our public forum. If your question includes sensitive information, you may send it instead to genom...@soe.ucsc.edu.
Lou Nassar
UCSC Genomics Institute
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