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  1. IGB
  2. IGBF-3106

Investigate: Is there a way to display track hub data on top of the already existing UCSC genomes?

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        • Type: Task
        • Status: Closed (View Workflow)
        • Priority: Major
        • Resolution: Done
        • Affects Version/s: None
        • Fix Version/s: None
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          Description

          Currently, when opening the quickload-derived trackhub (IGBF-3066) in the UCSC genome browser, only data files belonging to that trackhub can be loaded as tracks. Is there a way to load additional files for comparative purposes and to help explore new ideas about underlying biology?

          Track hub paper: https://pubmed.ncbi.nlm.nih.gov/24227676/ (from 2014 - it's the first paper; might be a little out of date)

          Note: Review any newer articles that might add this particular feature to the Track Hub system.

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              Task - A task that needs to be done. IGBF-3066 Create Track Hub for our human genome Quickload data

              • Major - Major loss of function.
              • Closed

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                pbadzuh Philip Badzuh (Inactive) added a comment -

                Based on my research, it appears that:

                • multiple track hubs can be "connected" to the UCSC genome browser at the same time. When a genome/assembly is opened in UCSC, every track hub that has data for that genome/assembly is loaded.
                • Default UCSC tracks for a genome/assembly are only shown when no 2bit file is specified in any of the hub.txt files of the connected track hubs.
                • I have removed the line in our hub.txt that pointed to the 2bit file for hg38, and now UCSC tracks are displayed in the same view with our trackhub, when hg38 is opened. I have created a UCSC browser session here, which demonstrates this and also includes an additional trackhub (ALFA Hub). Our trackhub files are listed under the "Experimental" section. This should be changed to "Quickload hub" once UCSC's cache has been cleared, since I recently updated the hub.txt shortLabel field from which this header is derived - it previously consisted of too many characters and was not read by UCSC, I'm guessing.
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                pbadzuh Philip Badzuh (Inactive) added a comment - Based on my research, it appears that: multiple track hubs can be "connected" to the UCSC genome browser at the same time. When a genome/assembly is opened in UCSC, every track hub that has data for that genome/assembly is loaded. Default UCSC tracks for a genome/assembly are only shown when no 2bit file is specified in any of the hub.txt files of the connected track hubs. I have removed the line in our hub.txt that pointed to the 2bit file for hg38, and now UCSC tracks are displayed in the same view with our trackhub, when hg38 is opened. I have created a UCSC browser session here , which demonstrates this and also includes an additional trackhub (ALFA Hub). Our trackhub files are listed under the "Experimental" section. This should be changed to "Quickload hub" once UCSC's cache has been cleared, since I recently updated the hub.txt shortLabel field from which this header is derived - it previously consisted of too many characters and was not read by UCSC, I'm guessing.

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                  • Assignee:
                    pbadzuh Philip Badzuh (Inactive)
                    Reporter:
                    pbadzuh Philip Badzuh (Inactive)
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                      Updated:
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