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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?

        Details

        • Type: Task
        • Status: Closed (View Workflow)
        • Priority: Major
        • Resolution: Done
        • Affects Version/s: None
        • Fix Version/s: None
        • Labels:
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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        Track hub paper: https://pubmed.ncbi.nlm.nih.gov/24227676/ (from 2014 - it's the first paper; might be a little out of date)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) created issue -
                pbadzuh Philip Badzuh (Inactive) made changes -
                Field Original Value New Value
                Epic Link IGBF-2831 [ 19524 ]
                pbadzuh Philip Badzuh (Inactive) made changes -
                Link This issue relates to IGBF-3066 [ IGBF-3066 ]
                ann.loraine Ann Loraine made changes -
                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? 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        Track hub paper: https://pubmed.ncbi.nlm.nih.gov/24227676/ (from 2014 - it's the first paper; might be a little out of date)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.
                ann.loraine Ann Loraine made changes -
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                ann.loraine Ann Loraine made changes -
                Rank Ranked higher
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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.
                Show
                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.
                pbadzuh Philip Badzuh (Inactive) made changes -
                Status To-Do [ 10305 ] In Progress [ 3 ]
                pbadzuh Philip Badzuh (Inactive) made changes -
                Status In Progress [ 3 ] Needs 1st Level Review [ 10005 ]
                ann.loraine Ann Loraine made changes -
                Sprint Spring 7 2022 Mar 28 - Apr 8 [ 142 ] Spring 7 2022 Mar 28 - Apr 8, Spring 8 2022 Apr 11 - Apr 22 [ 142, 143 ]
                ann.loraine Ann Loraine made changes -
                Rank Ranked higher
                ann.loraine Ann Loraine made changes -
                Status Needs 1st Level Review [ 10005 ] First Level Review in Progress [ 10301 ]
                ann.loraine Ann Loraine made changes -
                Status First Level Review in Progress [ 10301 ] Needs 1st Level Review [ 10005 ]
                ann.loraine Ann Loraine made changes -
                Status Needs 1st Level Review [ 10005 ] First Level Review in Progress [ 10301 ]
                ann.loraine Ann Loraine made changes -
                Status First Level Review in Progress [ 10301 ] Ready for Pull Request [ 10304 ]
                ann.loraine Ann Loraine made changes -
                Status Ready for Pull Request [ 10304 ] Pull Request Submitted [ 10101 ]
                ann.loraine Ann Loraine made changes -
                Status Pull Request Submitted [ 10101 ] Reviewing Pull Request [ 10303 ]
                ann.loraine Ann Loraine made changes -
                Status Reviewing Pull Request [ 10303 ] Merged Needs Testing [ 10002 ]
                ann.loraine Ann Loraine made changes -
                Status Merged Needs Testing [ 10002 ] Post-merge Testing In Progress [ 10003 ]
                ann.loraine Ann Loraine made changes -
                Resolution Done [ 10000 ]
                Status Post-merge Testing In Progress [ 10003 ] Closed [ 6 ]
                ann.loraine Ann Loraine made changes -
                Assignee Philip Badzuh [ pbadzuh ]

                  People

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