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    • Story Points:
      0.25
    • Sprint:
      Sprint 33, Sprint 34, Winter 2018 Sprint 2

      Description

      Zebrafish is one of the primary model organisms being studied by researchers. In September 2014 a new version of the genome was released. This new genome version needs to be added to IGB Quickload.

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            nfreese Nowlan Freese created issue -
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            Epic Link IGBF-236 [ 15233 ]
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            Epic Link IGBF-236 [ 15233 ]
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            Sprint Sprint 33, Sprint 34 [ 41, 42 ] Sprint 33, Sprint 34, Winter 2018 Sprint 2 [ 41, 42, 57 ]
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            ann.loraine Ann Loraine added a comment - - edited

            Follow this guide:

            "Add a new UCSC-managed genome to IGB Quickload"

            in Bioinformatics Data Manager google drive folder

            Show
            ann.loraine Ann Loraine added a comment - - edited Follow this guide: "Add a new UCSC-managed genome to IGB Quickload" in Bioinformatics Data Manager google drive folder
            ann.loraine Ann Loraine made changes -
            Assignee Jill Jenkins [ jill ]
            ann.loraine Ann Loraine made changes -
            Description Zebrafish is one of the primary model organisms being studied by researchers. In September 2014 a new version of the genome was released. This new genome version needs to be added to IGB Quickload.

            The new genome can be found here: http://hgdownload.soe.ucsc.edu/goldenPath/danRer10/bigZips/

            The new annotation can be found at the UCSC table browser: https://genome.ucsc.edu/cgi-bin/hgTables

            There are four different annotation files for this genome. I assume refseq is the default genome, however, it would be best to have the other three annotations as well.
            Zebrafish is one of the primary model organisms being studied by researchers. In September 2014 a new version of the genome was released. This new genome version needs to be added to IGB Quickload.



            Jill Jill Jenkins (Inactive) made changes -
            Summary Add new Zebrafish genome Add new zebrafish genome
            Jill Jill Jenkins (Inactive) made changes -
            Status Open [ 1 ] In Progress [ 3 ]
            ann.loraine Ann Loraine made changes -
            Labels Intermediate
            ann.loraine Ann Loraine made changes -
            Epic Link IGBF-1478 [ 17563 ]
            Jill Jill Jenkins (Inactive) made changes -
            Status In Progress [ 3 ] Needs 1st Level Review [ 10005 ]
            Jill Jill Jenkins (Inactive) made changes -
            Assignee Jill Jenkins [ jill ]
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            Jill Jill Jenkins (Inactive) added a comment -

            I have added the May 2017 assembly as per the user guide & tested in IGB.

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            Jill Jill Jenkins (Inactive) added a comment - I have added the May 2017 assembly as per the user guide & tested in IGB.
            ann.loraine Ann Loraine made changes -
            Status Needs 1st Level Review [ 10005 ] Reviewing [ 10301 ]
            ann.loraine Ann Loraine made changes -
            Assignee Ann Loraine [ aloraine ]
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            ann.loraine Ann Loraine added a comment -

            Committed D_rerio_May_2017 changes to subversion repo.
            Updated on:

            • renci host
            • uncc host
            • aws host
            Show
            ann.loraine Ann Loraine added a comment - Committed D_rerio_May_2017 changes to subversion repo. Updated on: renci host uncc host aws host
            ann.loraine Ann Loraine made changes -
            Resolution Done [ 10000 ]
            Status Reviewing [ 10301 ] Closed [ 6 ]
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            ann.loraine Ann Loraine added a comment -

            Re-assign to original developer

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            ann.loraine Ann Loraine added a comment - Re-assign to original developer
            ann.loraine Ann Loraine made changes -
            Assignee Ann Loraine [ aloraine ] Jill Jenkins [ jill ]
            ann.loraine Ann Loraine made changes -
            Workflow Loraine Lab Workflow [ 16053 ] Fall 2019 Workflow Update [ 20719 ]
            ann.loraine Ann Loraine made changes -
            Workflow Fall 2019 Workflow Update [ 20719 ] Revised Fall 2019 Workflow Update [ 21671 ]
            nfreese Nowlan Freese made changes -
            Fix Version/s 9.1.0 Major Release [ 10601 ]
            nfreese Nowlan Freese made changes -
            Link This issue relates to IGBF-3330 [ IGBF-3330 ]

              People

              • Assignee:
                Jill Jill Jenkins (Inactive)
                Reporter:
                nfreese Nowlan Freese
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                • Created:
                  Updated:
                  Resolved: