Details
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Type:
Task
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Status: Closed (View Workflow)
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Priority:
Major
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Resolution: Done
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Affects Version/s: None
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Fix Version/s: None
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Labels:None
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Story Points:4
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Epic Link:
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Sprint:Spring 3 2022 Jan 31 - Feb 11, Spring 4 2022 Feb 14 - Feb 25, Spring 5 2022 Feb 28 - Mar 11, Spring 6 2022 Mar 14 - Mar 25, Spring 7 2022 Mar 28 - Apr 8, Spring 8 2022 Apr 11 - Apr 22, Spring 9 2022 May 9, Summer 1 2022 May 23, Summer 2 2022 June 6, Summer 3 2022 June 21, Summer 4 2022 July 4, Summer 5 2022 July 18, Summer 6 2022 Aug 1
Description
One major goal of making IGB capable of viewing data from Track Hubs is to enable users to explore and analyze data using two genome browser instead of just one - Integrated Genome Browser and the UCSC Genome Browser.
We hypothesize that users will be able to notice and investigate new aspects of their data if they are able to use different genome browser tools to look at the same data. These new aspects could be anything - problems in data sets they were not aware of, problems with the browsers themselves, and, best of all, entirely new and undiscovered aspects of biology they were not previously aware of.
To emphasize and illustrate the above idea, let's create and deploy a Track Hub that will show genomes from the main IGB Quickload site, focusing on genome quickloads for important research organisms.
Create these track hubs "by hand", similar to what an ordinary (non-programmer) user would likely do. Take notes on issues and problems you encounter, as we will want to include these observations in papers and talks about the process.
For this task, create a Track Hub for the latest version of human genome, including data sets from all the quickloads available for that human genome (except Genome in a Bottle).
See this repository for possibly useful code and documentation regarding the quickload format: https://bitbucket.org/lorainelab/igbquickload/src/master/
Please see the attached file human_hub.zip. This contains the hub folder and all required configuration.
Quickload source
UCSC documentation used
Testing - needs to be deployed first