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  1. IGB
  2. IGBF-3693

Compare original ARE 120 minute flavonoid data to SRA Re-run data

        Details

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

          Description

          Use the compare SRA script made for marks data to compare the SRA submission to the original data.

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              Task - A task that needs to be done. IGBF-3639 Compare original mark-2022-timeseries data to SRA Re-run data

              • Major - Major loss of function.
              • Closed

                Activity

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                Mdavis4290 Molly Davis created issue -
                Mdavis4290 Molly Davis made changes -
                Field Original Value New Value
                Epic Link IGBF-2993 [ 21429 ]
                Mdavis4290 Molly Davis made changes -
                Link This issue relates to IGBF-3639 [ IGBF-3639 ]
                Mdavis4290 Molly Davis made changes -
                Status To-Do [ 10305 ] In Progress [ 3 ]
                Mdavis4290 Molly Davis made changes -
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                Mdavis4290 Molly Davis added a comment -

                Update: I found the original data on the cluster but only SL4 was run so for the comparison it will be made with the SRA SL4 run for right now. I am currently creating sample sheets for the original data and the rerun SRA data.

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                Mdavis4290 Molly Davis added a comment - Update : I found the original data on the cluster but only SL4 was run so for the comparison it will be made with the SRA SL4 run for right now. I am currently creating sample sheets for the original data and the rerun SRA data.
                ann.loraine Ann Loraine made changes -
                Sprint Spring 8 [ 192 ] Spring 8, Spring 9 [ 192, 193 ]
                ann.loraine Ann Loraine made changes -
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                Mdavis4290 Molly Davis added a comment -

                Branch: https://bitbucket.org/mdavis4290/molly5-flavonoid-rnaseq/branch/IGBF-3693

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                Mdavis4290 Molly Davis added a comment - Branch : https://bitbucket.org/mdavis4290/molly5-flavonoid-rnaseq/branch/IGBF-3693
                Mdavis4290 Molly Davis made changes -
                Assignee Molly Davis [ molly ]
                Mdavis4290 Molly Davis made changes -
                Status In Progress [ 3 ] Needs 1st Level Review [ 10005 ]
                Mdavis4290 Molly Davis made changes -
                Assignee Ann Loraine [ aloraine ]
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                ann.loraine Ann Loraine added a comment -

                Change requests:

                • Move excel and html MultiQC report files to a new directory "Documentation"
                • Where is the "multiQC report for the newly run "SRR" samples? We need two multi-qc reports: one showing how the pipeline ran on the original sequence files and one showing how the pipeline ran on the newly downloaded samples
                Show
                ann.loraine Ann Loraine added a comment - Change requests: Move excel and html MultiQC report files to a new directory "Documentation" Where is the "multiQC report for the newly run "SRR" samples? We need two multi-qc reports: one showing how the pipeline ran on the original sequence files and one showing how the pipeline ran on the newly downloaded samples
                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 ] To-Do [ 10305 ]
                ann.loraine Ann Loraine made changes -
                Assignee Ann Loraine [ aloraine ] Molly Davis [ molly ]
                Mdavis4290 Molly Davis made changes -
                Status To-Do [ 10305 ] In Progress [ 3 ]
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                Mdavis4290 Molly Davis added a comment -

                Branch: https://bitbucket.org/mdavis4290/molly5-flavonoid-rnaseq/branch/IGBF-3693b

                Note: Moved the files to a new documentation folder. The SRA mutliQC reports were already created and added to the repo prior to adding the original data one from the cluster.

                Show
                Mdavis4290 Molly Davis added a comment - Branch : https://bitbucket.org/mdavis4290/molly5-flavonoid-rnaseq/branch/IGBF-3693b Note: Moved the files to a new documentation folder. The SRA mutliQC reports were already created and added to the repo prior to adding the original data one from the cluster.
                Mdavis4290 Molly Davis made changes -
                Assignee Molly Davis [ molly ] Ann Loraine [ aloraine ]
                Mdavis4290 Molly Davis made changes -
                Status In Progress [ 3 ] Needs 1st Level Review [ 10005 ]
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                Mdavis4290 Molly Davis added a comment - - edited

                Updated Branch with output file line added:

                https://bitbucket.org/mdavis4290/molly5-flavonoid-rnaseq/commits/24714cd3053b54e5749b2fbc1ce02c16bcb53db8

                Show
                Mdavis4290 Molly Davis added a comment - - edited Updated Branch with output file line added : https://bitbucket.org/mdavis4290/molly5-flavonoid-rnaseq/commits/24714cd3053b54e5749b2fbc1ce02c16bcb53db8
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                ann.loraine Ann Loraine added a comment -

                Above PR is merged.

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                ann.loraine Ann Loraine added a comment - Above PR is merged.
                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 ]
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                ann.loraine Ann Loraine added a comment -

                Proceeding to test by re-running checking code.

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                ann.loraine Ann Loraine added a comment - Proceeding to test by re-running checking code.
                ann.loraine Ann Loraine made changes -
                Sprint Spring 8, Spring 9 [ 192, 193 ] Spring 8, Spring 9, Spring 10 [ 192, 193, 194 ]
                ann.loraine Ann Loraine made changes -
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                ann.loraine Ann Loraine added a comment -

                The new SRA meta-data is correct so far as we can tell. Moving to Done.

                Show
                ann.loraine Ann Loraine added a comment - The new SRA meta-data is correct so far as we can tell. Moving to Done.
                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 ]

                  People

                  • Assignee:
                    ann.loraine Ann Loraine
                    Reporter:
                    Mdavis4290 Molly Davis
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                    Dates

                    • Created:
                      Updated:
                      Resolved: