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  1. IGB
  2. IGBF-3144

Make annots.xml for RNA-Seq junction, alignment, and coverage graphs

        Details

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

          Description

          This is needed to deploy the new data files for visualization in IGB.

            Attachments

              Issue Links

              is blocked by

              Task - A task that needs to be done. IGBF-3040 Create samplesheet with SRR run identifiers and experimental attributes

              • Major - Major loss of function.
              • Closed

              Task - A task that needs to be done. IGBF-3143 Run RNA-Seq data processing pipeline on positive splicing control and experimental samples

              • Major - Major loss of function.
              • Closed

              Task - A task that needs to be done. IGBF-3162 Generate scaled coverage graphs for RNA-Seq alignments

              • Major - Major loss of function.
              • Closed
              relates to

              Task - A task that needs to be done. IGBF-3230 Visualize alternative splicing events

              • Major - Major loss of function.
              • Closed

                Activity

                Ascending order - Click to sort in descending order
                ann.loraine Ann Loraine created issue -
                ann.loraine Ann Loraine made changes -
                Field Original Value New Value
                Epic Link IGBF-2993 [ 21429 ]
                ann.loraine Ann Loraine made changes -
                Link This issue is blocked by IGBF-3143 [ IGBF-3143 ]
                ann.loraine Ann Loraine made changes -
                Description * Run code to generate scaled coverage graphs (ask Ann for details)
                * Run code to generate function files (ask Ann for details)
                * Generate annots.xml files for IGB Quickload for visualization (ask Ann for details)                 		* Run code to generate scaled coverage graphs (ask Ann for details)
                * Run code to generate junctions files (ask Ann for details)
                * Generate annots.xml files for IGB Quickload for visualization (ask Ann for details)
                ann.loraine Ann Loraine made changes -
                Story Points 2 3
                ann.loraine Ann Loraine made changes -
                Sprint Summer 5 2022 July 18 [ 151 ] Summer 5 2022 July 18, Summer 6 2022 Aug 1 [ 151, 152 ]
                ann.loraine Ann Loraine made changes -
                Rank Ranked higher
                ann.loraine Ann Loraine made changes -
                Sprint Summer 5 2022 July 18, Summer 6 2022 Aug 1 [ 151, 152 ] Summer 5 2022 July 18, Summer 6 2022 Aug 1, Fall 1 2022 Aug 15 [ 151, 152, 153 ]
                ann.loraine Ann Loraine made changes -
                Rank Ranked higher
                ann.loraine Ann Loraine made changes -
                Description * Run code to generate scaled coverage graphs (ask Ann for details)
                * Run code to generate junctions files (ask Ann for details)
                * Generate annots.xml files for IGB Quickload for visualization (ask Ann for details)                 		* Run code to generate scaled coverage graphs - see https://bitbucket.org/hotpollen/flavonoid-rnaseq/src/c53c3b94da5a/src/bamCoverage.sh
                * Run code to generate junctions files (ask Ann for details)
                * Generate annots.xml files for IGB Quickload for visualization (ask Ann for details)
                ann.loraine Ann Loraine made changes -
                Summary Run post-processing on alt splicing RNA-Seq samples Make annots.xml for RNA-Seq junction, alignment, and coverage graphs
                ann.loraine Ann Loraine made changes -
                Description * Run code to generate scaled coverage graphs - see https://bitbucket.org/hotpollen/flavonoid-rnaseq/src/c53c3b94da5a/src/bamCoverage.sh
                * Run code to generate junctions files (ask Ann for details)
                * Generate annots.xml files for IGB Quickload for visualization (ask Ann for details)
                ann.loraine Ann Loraine made changes -
                Description This is needed to deploy the new data files for visualization in IGB.
                ann.loraine Ann Loraine made changes -
                Link This issue is blocked by IGBF-3162 [ IGBF-3162 ]
                ann.loraine Ann Loraine made changes -
                Link This issue is blocked by IGBF-3161 [ IGBF-3161 ]
                ann.loraine Ann Loraine made changes -
                Sprint Summer 5 2022 July 18, Summer 6 2022 Aug 1, Fall 1 2022 Aug 15 [ 151, 152, 153 ] Summer 5 2022 July 18, Summer 6 2022 Aug 1, Fall 2 2022 Sep 5 [ 151, 152, 154 ]
                ann.loraine Ann Loraine made changes -
                Status To-Do [ 10305 ] In Progress [ 3 ]
                ann.loraine Ann Loraine made changes -
                Status In Progress [ 3 ] To-Do [ 10305 ]
                ann.loraine Ann Loraine made changes -
                Status To-Do [ 10305 ] In Progress [ 3 ]
                ann.loraine Ann Loraine made changes -
                Assignee Ann Loraine [ aloraine ]
                ann.loraine Ann Loraine made changes -
                Link This issue is blocked by IGBF-3173 [ IGBF-3173 ]
                ann.loraine Ann Loraine made changes -
                Sprint Summer 5 2022 July 18, Summer 6 2022 Aug 1, Fall 2 2022 Sep 5 [ 151, 152, 154 ] Summer 5 2022 July 18, Summer 6 2022 Aug 1 [ 151, 152 ]
                ann.loraine Ann Loraine made changes -
                Status In Progress [ 3 ] To-Do [ 10305 ]
                ann.loraine Ann Loraine made changes -
                Assignee Ann Loraine [ aloraine ]
                ann.loraine Ann Loraine made changes -
                Link This issue is blocked by IGBF-3173 [ IGBF-3173 ]
                ann.loraine Ann Loraine made changes -
                Link This issue is blocked by IGBF-3040 [ IGBF-3040 ]
                ann.loraine Ann Loraine made changes -
                Sprint Summer 5 2022 July 18, Summer 6 2022 Aug 1 [ 151, 152 ] Summer 5 2022 July 18, Summer 6 2022 Aug 1, Fall 6 2022 Nov 7 [ 151, 152, 158 ]
                ann.loraine Ann Loraine made changes -
                Assignee Ann Loraine [ aloraine ]
                ann.loraine Ann Loraine made changes -
                Status To-Do [ 10305 ] In Progress [ 3 ]
                ann.loraine Ann Loraine made changes -
                Status In Progress [ 3 ] To-Do [ 10305 ]
                ann.loraine Ann Loraine made changes -
                Status To-Do [ 10305 ] In Progress [ 3 ]
                ann.loraine Ann Loraine made changes -
                Attachment screenshot-1.png [ 17566 ]
                ann.loraine Ann Loraine made changes -
                Status In Progress [ 3 ] 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 -
                Link This issue relates to IGBF-3230 [ IGBF-3230 ]

                  People

                  • Assignee:
                    ann.loraine Ann Loraine
                    Reporter:
                    ann.loraine Ann Loraine
                  • Votes:
                    0 Vote for this issue
                    Watchers:
                    1 Start watching this issue

                    Dates

                    • Created:
                      Updated:
                      Resolved: