Unrecognised BigBed file format in UCSC Genome Browser

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Hanyun Zheng

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Jan 23, 2017, 11:39:57 AM1/23/17
to gen...@soe.ucsc.edu
Hello,
I am a user of UCSC Genome Browser and I have converted a BED file into BigBed and uploaded it onto OneDrive. However, using the URL of the BigBed file, when I tried to submit on the UCSC Genome Browser, it says the following error message:
Error It appears that you are directly uploading binary data in an unrecognized format (https://wehieduau-my.sharepoint.com/personal/zheng_h_wehi_edu_au/_layouts/15/download.aspx?docid=10a342114ebff4388a9a30f78e21d6a66&authkey=AbBtq7uoY_awldO_GdoKJm8). For custom track formatting information, please see custom track documentation.


Btw, this is the link for which you can access the BigBed file:

https://wehieduau-my.sharepoint.com/personal/zheng_h_wehi_edu_au/_layouts/15/guestaccess.aspx?docid=10a342114ebff4388a9a30f78e21d6a66&authkey=AbBtq7uoY_awldO_GdoKJm8

So I am just wondering that, do I need to do some other conversions before getting the URL? Any help would be much appreciated:)

Kind regards,
Jessica (Hanyun Zheng)

Brian Lee

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Jan 23, 2017, 1:15:28 PM1/23/17
to Hanyun Zheng, gen...@soe.ucsc.edu
Dear Jessica,

Thank you for using the UCSC Genome Browser and your question about bigBed data in the Browser.

Unfortunately it looks like the link you provided is private, but also it likely is not enabled to allow repeated data requests  needed from servers to host bigBed data files. This is often the case for free data storage services, but a solution exists for biologists at CyVerse, which is not run by UCSC, all questions about CyVerse must be directed to their customer support. 

When I tried your link I observed this response: Sorry, you cannot access this document. Please contact the person who shared it with you.  However, I also used the command-line tool "curl" with the option -I to see if the link would support "byte-range" requests and it does not appear that One Drive does.  Many free data hosting sites like Google Drive or DropBox and apparently One Drive will not support byte-range requests that are needed to display the bigBed data in the browser.  

There is, however, a free storage service offered by CyVerse.  CyVerse previously was called iPlant, and provided services to the plant genomics community.  NSF has funded their free services to the entire genomics community and you can host your data there without cost.

Here is an example of a bigBed hosted at CyVerse: 

To load data at CyVerse, first you create an account and then use their "Discovery Environment" to upload data: http://de.cyverse.org

Once you have uploaded data, you have to give it a "Info-Type:" that will enable to access a "Send to Genome Browser" link under the "Share" column.  The resulting link is the kind of link that will successfully support byte-range requests and allow viewing of the data at UCSC.

Here are some pictures of the CyVerse Discover Environment and where to click to obtain the "Send to Genom Browser" links:
Inline image 3Inline image 4


Thank you again for your inquiry and using the UCSC Genome Browser. If you have any further questions, please reply to gen...@soe.ucsc.edu. All messages sent to that address are archived on a publicly-accessible forum. If your question includes sensitive data, you may send it instead to genom...@soe.ucsc.edu.

All the best,

Brian Lee
UCSC Genomics Institute




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