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  1. IGB
  2. IGBF-3711

Set up SRA-downloaded Muday datasets in the RNA-Seq Quickload

        Details

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

          Description

          The workshop that we'll be giving at ASPB will be focusing on Gloria Muday's tomato data from her upcoming publication ("Flavonols improve thermotolerance in tomato pollen during germination and tube elongation by maintaining ROS homeostasis").

          Task: Set up the SRA-downloaded dataset (including sequence alignments, coverage graphs, and junction files) in the tomato RNA-Seq Quickload so that we can use that Quickload for the ASPB workshop materials. This will require fixing the ongoing SRA sample labeling problem.

            Attachments

              Issue Links

              relates to

              Organization Issue - IGB manual IGBF-3714 Fix title fields in the SL5 annots.xml file

              • Major - Major loss of function.
              • Closed

              Task - A task that needs to be done. IGBF-3673 Draft key concepts/topics to be covered in the ASPB 2024 workshop

              • Critical - Crashes, loss of data, severe memory leak.
              • Closed

              Task - A task that needs to be done. IGBF-3672 Draft a workshop outline for ASPB 2024

              • Major - Major loss of function.
              • Closed

                Activity

                Ascending order - Click to sort in descending order
                pkulzer Paige Kulzer created issue -
                pkulzer Paige Kulzer made changes -
                Field Original Value New Value
                Epic Link IGBF-1395 [ 17470 ]
                pkulzer Paige Kulzer made changes -
                Link This issue relates to IGBF-3673 [ IGBF-3673 ]
                pkulzer Paige Kulzer made changes -
                Link This issue relates to IGBF-3672 [ IGBF-3672 ]
                ann.loraine Ann Loraine made changes -
                Rank Ranked higher
                pkulzer Paige Kulzer made changes -
                Link This issue relates to IGBF-3714 [ IGBF-3714 ]
                ann.loraine Ann Loraine made changes -
                Status To-Do [ 10305 ] In Progress [ 3 ]
                Hide
                Permalink
                ann.loraine Ann Loraine added a comment -

                Update:

                • Data sets needed for the workshop are now available under the "RNA-Seq" data source provided by default with IGB.
                • There is now no longer any need to add the "hotpollen" Quickload site to view these data
                • I fixed the bug that was affecting the Muday Lab data set

                To test:

                • Visit the latest and next-to-latest genome assemblies available for tomato S. lycopersicum
                • Confirm that you can now load and view all data sets without error from the data folder named "Muday Lab - pollen tube, anthocyanin reduced (are) heat stress, 15 - 75 min (SRP460750)" under the "RNA-Seq" data source
                Show
                ann.loraine Ann Loraine added a comment - Update: Data sets needed for the workshop are now available under the "RNA-Seq" data source provided by default with IGB. There is now no longer any need to add the "hotpollen" Quickload site to view these data I fixed the bug that was affecting the Muday Lab data set To test: Visit the latest and next-to-latest genome assemblies available for tomato S. lycopersicum Confirm that you can now load and view all data sets without error from the data folder named "Muday Lab - pollen tube, anthocyanin reduced (are) heat stress, 15 - 75 min (SRP460750)" under the "RNA-Seq" data source
                ann.loraine Ann Loraine made changes -
                Status In Progress [ 3 ] Needs 1st Level Review [ 10005 ]
                ann.loraine Ann Loraine made changes -
                Assignee Ann Loraine [ aloraine ] Paige Kulzer [ pkulzer ]
                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 -
                Sprint Spring 9 [ 193 ] Spring 9, Spring 10 [ 193, 194 ]
                ann.loraine Ann Loraine made changes -
                Rank Ranked higher
                pkulzer Paige Kulzer made changes -
                Status Merged Needs Testing [ 10002 ] Post-merge Testing In Progress [ 10003 ]
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                Permalink
                pkulzer Paige Kulzer added a comment -

                All data sets from the Muday Lab folder load without error against the SL4 and SL5 genomes. The default FG color of each track correctly corresponds to the sample's species and experimental temperature. Available data is listed in an order that makes sense.

                Moving to done.

                Show
                pkulzer Paige Kulzer added a comment - All data sets from the Muday Lab folder load without error against the SL4 and SL5 genomes. The default FG color of each track correctly corresponds to the sample's species and experimental temperature. Available data is listed in an order that makes sense. Moving to done.
                pkulzer Paige Kulzer made changes -
                Resolution Done [ 10000 ]
                Status Post-merge Testing In Progress [ 10003 ] Closed [ 6 ]
                pkulzer Paige Kulzer made changes -
                Assignee Paige Kulzer [ pkulzer ] Ann Loraine [ aloraine ]

                  People

                  • Assignee:
                    ann.loraine Ann Loraine
                    Reporter:
                    pkulzer Paige Kulzer
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                    Dates

                    • Created:
                      Updated:
                      Resolved: