bigBed File to web-accessible ?

[Zaman, Tanzila]

Hello,

 

I hope this finds you well!

 

I am trying to create a custom track using mice dataset. I have created my bb file which is under longleaf, a linux based computing system. I am having trouble understanding this part. What does this mean, where can I get more guidance?

 

Step 6. Move the newly created bigBed file (myBigBed.bb) to a web-accessible http, https, or ftp location.

 

Regards,

Tanzila Zaman

Project Manager-Contract Study

High-Throughput Sequencing Facility (HTSF)

University of North Carolina-Chapel Hill

Genome Sciences Building

250 Bell Tower Dr.

Chapel Hill, NC

 

Email:tanz...@live.unc.edu
Phone: (919) 445-1048

 

[Daniel Schmelter]

Hello Tanzila,

Thank you for using the Genome Browser and for your question about bigBed files.

All binary indexed data formats (like bigBed) require external hosting from a web-accessible server to be visualized as a custom track. This means that the files need to be uploaded to somewhere online that can be accessed through a link, e.g. http://genome.ucsc.edu/goldenPath/help/examples/bigBedExample.bb. The advantage is that only the data needed to display a particular region are transferred to the Genome Browser server, not the entire file. This allows for a much faster display and requires far less processing for our servers.

The bigBed format page describes the bigBed file hosting requirement in the first paragraph:

https://genome.ucsc.edu/goldenPath/help/bigBed.html

A number of free web-hosting options are available like GitHub and CyVerse. Universities often offer web-hosting to their affiliates too. Certain sites will not work for bigBed file hosting because they prohibit partial file requests, like Google Drive and DropBox. More information about web-hosting can be found below, including examples for hosting on GitHub and CyVerse:

https://genome.ucsc.edu/goldenPath/help/hgTrackHubHelp.html#Hosting

I hope this was helpful. If you have any more questions, please reply-all to gen...@soe.ucsc.edu. All messages sent to that address are publicly archived. If your question includes sensitive data, please reply-all to genom...@soe.ucsc.edu.
All the best,

Daniel Schmelter
UCSC Genome Browser

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[Zaman, Tanzila]

Hello,

 

Thank you for the information.

 

I am getting the following errors:

 

 

Regards,

Tanzila Zaman

Project Manager-Contract Study

High-Throughput Sequencing Facility (HTSF)

University of North Carolina-Chapel Hill

Genome Sciences Building

250 Bell Tower Dr.

Chapel Hill, NC

 

Email:tanz...@live.unc.edu
Phone: (919) 445-1048

 

[Daniel Schmelter]

Hello Tanzila,

We are glad you got your files in a web-accessible location. Unfortunately, there appear to be some access restrictions that prevent the Genome Browser from viewing at the link. Hopefully, it is viewable from your computer, but to us, that link gives an error:

This site can’t be reached trackhub.its.unc.edu’s server IP address could not be found.

This is often because of network restrictions that are set up to prevent anyone outside of your institution's IP ranges to view those files. This firewall blocks the Genome Browser from retrieving the data at that link and thus prevents it from displaying your Custom Tracks. You may want to contact your System Administrators and request that they allow access to the IP addresses 128.114.119.132 and 128.114.119.131

I hope this was helpful. If you have any more questions, please reply-all to gen...@soe.ucsc.edu. All messages sent to that address are publicly archived. If your question includes sensitive data, please reply-all to genom...@soe.ucsc.edu.
All the best,

Daniel Schmelter
UCSC Genome Browser

[Zaman, Tanzila]

Hello,

 

My admin has allowed the folder this is located to be web-accessible. I am still having the following issues:

[Matthew Speir]

Hello, Tanzila. 

The error you are seeing is due to the fact that you have misspelled "longLabel" in your hub.txt:

hub mice
shortLabel mice track
longLabll mice data frm POSTAR using annotatation of mm10
email tanz...@live.unc.edu
descriptionUrl mice.html

The "longLabll" above should be "longLabel". The spelling, capitalization, and formatting of all the settings in your hub.txt, genomes.txt, and trackDb.txt files is important and, as you can see, will not function if something is misspelled or wrong, so please double check them before attempting to load them into the Genome Browser and after you get errors such as the one in your email. Additionally, you will need a "genomesFile" line in your hub.txt file that points to a "genomes.txt" file that contains information about the assemblies covered. More information about hub structure can be found in this quick start guide for basic hubs: http://genome.ucsc.edu/goldenPath/help/hubQuickStart.html. More detailed information and links to other hub resources can be found on our Track Hub User Guide: http://genome.ucsc.edu/goldenPath/help/hgTrackHubHelp.html. 

Additionally, to help with the process of double checking your hubs for issues before visualizing them, you can use the command-line utility hubCheck or the "Hub Development" tab where you load your hub URLs: https://genome.ucsc.edu/cgi-bin/hgHubConnect?#hubDeveloper. The hubCheck utility can be obtained from our downloads server for Linux, http://hgdownload.soe.ucsc.edu/admin/exe/linux.x86_64/hubCheck, or Mac OSX, http://hgdownload.soe.ucsc.edu/admin/exe/macOSX.x86_64/hubCheck. Both of these tools can help identify invalid settings, poor trackDb structure, and more. 

I hope this is helpful. 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 Google Groups forum. If your question includes sensitive data, you may send it instead to genom...@soe.ucsc.edu.

Training videos & resources: http://genome.ucsc.edu/training/index.html

Want to share the Browser with colleagues? Host a workshop: http://bit.ly/ucscTraining

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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.

To view this discussion on the web visit https://groups.google.com/a/soe.ucsc.edu/d/msgid/genome-mirror/MN2PR03MB4895906804483EC5AF09B63BFF490%40MN2PR03MB4895.namprd03.prod.outlook.com.