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  1. IGB
  2. IGBF-3286

Reorganize flavonoid rnaseq repo to accommodate new datasets

        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

          We have a new dataset from the Muday lab with experimental conditions similar to the first one we processed. However, a lot of the code in the repository is written as though there will only ever be one dataset. This is very confusing.

          I will reorganize the repo and file names to make the repository easier to understand.

          Repository:

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              ann.loraine Ann Loraine added a comment -

              [~molly] and I reviewed the new structure. Moving to Done.

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              ann.loraine Ann Loraine added a comment - [~molly] and I reviewed the new structure. Moving to Done.
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              ann.loraine Ann Loraine added a comment -

              Re-org complete, for now. Moving to "needs first level review".

              [~molly] : please take a look and let me know if everything makes sense or if you have any questions.

              All changes are merged into the main branch.

              Please note:

              There is a new "counts" file made from the original "salmon" file with two big changes:

              • it has gene descriptions from SL5
              • it uses sample codes as column headings
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              ann.loraine Ann Loraine added a comment - Re-org complete, for now. Moving to "needs first level review". [~molly] : please take a look and let me know if everything makes sense or if you have any questions. All changes are merged into the main branch. Please note: There is a new "counts" file made from the original "salmon" file with two big changes: it has gene descriptions from SL5 it uses sample codes as column headings
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              ann.loraine Ann Loraine added a comment -

              Adding code to write a new version of counts file containing gene descriptions and renaming columns to match sample codes in https://bitbucket.org/hotpollen/flavonoid-rnaseq/src/main/ExternalDataSets/muday-144_sample_sheet.xlsx.

              Show
              ann.loraine Ann Loraine added a comment - Adding code to write a new version of counts file containing gene descriptions and renaming columns to match sample codes in https://bitbucket.org/hotpollen/flavonoid-rnaseq/src/main/ExternalDataSets/muday-144_sample_sheet.xlsx .
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              ann.loraine Ann Loraine added a comment -

              Please review commits with this Jira issue tag in commit message.

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              ann.loraine Ann Loraine added a comment - Please review commits with this Jira issue tag in commit message.

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                • Assignee:
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                  Reporter:
                  ann.loraine Ann Loraine
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                  • Created:
                    Updated:
                    Resolved: