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  1. IGB
  2. IGBF-3714

Fix title fields in the SL5 annots.xml file

        Details

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

          Description

          Situation: I was attempting to add several coverage graph tracks from the "PT time GM lab" folder in the RNA-Seq Quickload when I encountered a "Cannot add same feature" error. The track I was trying to add was titled "A.28.75.8 cool ARE pollen tube 75 min scaled coverage" but the error shows that that track points to a different data file than what it's titled ("8-are-75-min-34C.scaled.bedgraph.gz", see attached).

          I took a look through the SL5 annots.xml file and have found that all of the .8 and .9 replicates from the Muday study have incorrect titles (see attached). I only pulled out lines from annots.xml that pertained to coverage graphs to create the attached spreadsheet, but please note that ALL file types (.bam, .bedgraph.gz, and .bed.gz) have this mislabeling issue with these replicates.

          Task: Correct the title field in the SL5 annots.xml file for all .8 and .9 replicates from the Muday study.

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              relates to

              Task - A task that needs to be done. IGBF-3711 Set up SRA-downloaded Muday datasets in the RNA-Seq Quickload

              • Major - Major loss of function.
              • Closed

                Activity

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                pkulzer Paige Kulzer created issue -
                pkulzer Paige Kulzer made changes -
                Field Original Value New Value
                Epic Link IGBF-2993 [ 21429 ]
                pkulzer Paige Kulzer made changes -
                Description Situation: I was attempting to add several coverage graph tracks from the "PT time GM lab" folder in the RNA-Seq Quickload when I encountered a "Cannot add same feature" error. The track I was trying to add was titled "A.28.75.8 cool ARE pollen tube 75 min scaled coverage" but the error shows that that track points to a different data file than what it's titled ("8-are-75-min-34C.scaled.bedgraph.gz", see attached).

                I took a look through the SL5 annots.xml file and have found that all of the .8 and .9 replicates have incorrect titles (see attached). I only pulled out lines from annots.xml that pertained to coverage graphs to create the attached spreadsheet, but please note that *ALL* file types (.bam, .bedgraph.gz, and .bed.gz) have this mislabeling issue with these replicates.

                Task: Correct the title field in the SL5 annots.xml file for all .8 and .9 replicates.                 		Situation: I was attempting to add several coverage graph tracks from the "PT time GM lab" folder in the RNA-Seq Quickload when I encountered a "Cannot add same feature" error. The track I was trying to add was titled "A.28.75.8 cool ARE pollen tube 75 min scaled coverage" but the error shows that that track points to a different data file than what it's titled ("8-are-75-min-34C.scaled.bedgraph.gz", see attached).

                I took a look through the SL5 annots.xml file and have found that all of the .8 and .9 replicates from the Muday study have incorrect titles (see attached). I only pulled out lines from annots.xml that pertained to coverage graphs to create the attached spreadsheet, but please note that *ALL* file types (.bam, .bedgraph.gz, and .bed.gz) have this mislabeling issue with these replicates.

                Task: Correct the title field in the SL5 annots.xml file for all .8 and .9 replicates from the Muday study.
                pkulzer Paige Kulzer made changes -
                Assignee Ann Loraine [ aloraine ]
                pkulzer Paige Kulzer made changes -
                Link This issue relates to IGBF-3711 [ IGBF-3711 ]
                ann.loraine Ann Loraine made changes -
                Status To-Do [ 10305 ] In Progress [ 3 ]
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                ann.loraine Ann Loraine added a comment -

                I fixed the code that makes the annots.xml files and redeployed the Quickload site.

                For review, see:

                Show
                ann.loraine Ann Loraine added a comment - I fixed the code that makes the annots.xml files and redeployed the Quickload site. For review, see: Repository: https://bitbucket.org/hotpollen/genome-browser-visualization/src/main/ Code changes affect method renameSamples in: https://bitbucket.org/hotpollen/genome-browser-visualization/src/main/makeAnnotsXml.py
                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 -
                Assignee Ann Loraine [ aloraine ]
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                ann.loraine Ann Loraine added a comment -

                Attention: Paige Kulzer
                Please test and make sure the issue you identified is no longer a problem.

                Show
                ann.loraine Ann Loraine added a comment - Attention: Paige Kulzer Please test and make sure the issue you identified is no longer a problem.
                ann.loraine Ann Loraine made changes -
                Assignee Paige Kulzer [ pkulzer ]
                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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                pkulzer Paige Kulzer added a comment -

                All scaled coverage graph replicates are now able to be loaded without error. Moving to done.

                Show
                pkulzer Paige Kulzer added a comment - All scaled coverage graph replicates are now able to be loaded without error. 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: