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  1. IGB
  2. IGBF-3315

Improve BED file representing annotations for the T-DNA construct used to create F3H-OX3

        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

          Suggestions for improvement - to make the image look nicer:
          Pick some pretty colors to distinguish protein-coding genes (e.g., KanR, F3H) from the other features. Currently, all the features have the same color (RGB code 0,0,255). If you do that, then we can make a very nice visualization by turning on the "Color by RGB" feature in the track.
          Copy the values from field 14 into field 13.
          You can curate field 14 a bit more, by judiciously copying over some of the text annotations from each feature in the original GenBank file.

          Find the bed file in bitbucket: https://bitbucket.org/hotpollen/flavonoid-rnaseq/src/main/ExternalDataSets/pK7WG2-F3H-OX3.bed

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              Task - A task that needs to be done. IGBF-3327 Improve BED file again representing annotations for the T-DNA construct used to create F3H-OX3

              • Major - Major loss of function.
              • Closed

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                Mdavis4290 Molly Davis added a comment -

                Branch: https://bitbucket.org/mdavis4290/molly-flavonoid-rnaseq/branch/IGBF-3315

                Review:

                • Are the colors appropriate?
                • Has the 13th and 14th columns been switched and the descriptions column improved in detail?
                Show
                Mdavis4290 Molly Davis added a comment - Branch: https://bitbucket.org/mdavis4290/molly-flavonoid-rnaseq/branch/IGBF-3315 Review: Are the colors appropriate? Has the 13th and 14th columns been switched and the descriptions column improved in detail?
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                ann.loraine Ann Loraine added a comment -

                Getting BED file from branch via URL:

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                ann.loraine Ann Loraine added a comment - Getting BED file from branch via URL: https://bitbucket.org/mdavis4290/molly-flavonoid-rnaseq/src/IGBF-3315/ExternalDataSets/pK7WG2-F3H-OX3.bed
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                ann.loraine Ann Loraine added a comment -

                Functional Review:

                • Opened the plasmid sequence as a new "Custom Genome"
                • Opened plasmid bed file version 2 on topic branch
                • Changed "Color by" parameter to "R,G,B" for the plasmid bed file track
                • Made image - see attached

                Could be improved. If we do that, we should do it in a separate ticket after closing this one.

                • Title (field 13) could be better. This is what appears in the "Selection Info" box in the upper right corner when a user clicks on a thing.
                • Id (field 4) for "ColE1/pMB1/..." should be shorter. Move some of this information to the "Description" (field 14)
                • Things that come in pairs (e.g., LB and RB) should probably be the same color.
                Show
                ann.loraine Ann Loraine added a comment - Functional Review: Opened the plasmid sequence as a new "Custom Genome" Opened plasmid bed file version 2 on topic branch Changed "Color by" parameter to "R,G,B" for the plasmid bed file track Made image - see attached Could be improved. If we do that, we should do it in a separate ticket after closing this one. Title (field 13) could be better. This is what appears in the "Selection Info" box in the upper right corner when a user clicks on a thing. Id (field 4) for "ColE1/pMB1/..." should be shorter. Move some of this information to the "Description" (field 14) Things that come in pairs (e.g., LB and RB) should probably be the same color.
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                ann.loraine Ann Loraine added a comment -

                Code is fine.
                Please rebase topic branch on team repository's main branch. Pull request should update.
                Moving to "ready for pull request". When branch is updated, please move to "pull request submitted" and un-assign it.

                Show
                ann.loraine Ann Loraine added a comment - Code is fine. Please rebase topic branch on team repository's main branch. Pull request should update. Moving to "ready for pull request". When branch is updated, please move to "pull request submitted" and un-assign it.
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                Mdavis4290 Molly Davis added a comment - - edited

                Rebasing: 

                git checkout IGBF-3315
git rebase main
git push --force origin IGBF-3315

                Made a new pull request:
                https://bitbucket.org/hotpollen/flavonoid-rnaseq/pull-requests/13

                Show
                Mdavis4290 Molly Davis added a comment - - edited Rebasing: git checkout IGBF-3315 git rebase main git push --force origin IGBF-3315 Made a new pull request: https://bitbucket.org/hotpollen/flavonoid-rnaseq/pull-requests/13
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                ann.loraine Ann Loraine added a comment -

                Merged.

                Moving DONE without any further testing.

                Show
                ann.loraine Ann Loraine added a comment - Merged. Moving DONE without any further testing.

                  People

                  • Assignee:
                    Mdavis4290 Molly Davis
                    Reporter:
                    Mdavis4290 Molly Davis
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                    • Created:
                      Updated:
                      Resolved: