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  1. IGB
  2. IGBF-3627

Create sample sheet for SRP460750

        Details

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

          Description

          Muday-144 experiment has been submitted to SRA and rerun with nextflow. A sanity check was performed on the original data and the rerun SRA data to ensure the submission to NCBI was correct. The next step is adding the SRA data to IGB Quickload. To do this a sample sheet is required.

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              relates to

              Task - A task that needs to be done. IGBF-3507 Re-run Nextflow Muday time course data with SL4 and data downloaded from SRA

              • Major - Major loss of function.
              • Closed

              Task - A task that needs to be done. IGBF-3596 Compare original Muday flavonoid 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-3596 [ IGBF-3596 ]
                Mdavis4290 Molly Davis made changes -
                Link This issue relates to IGBF-3507 [ IGBF-3507 ]
                Mdavis4290 Molly Davis made changes -
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                Mdavis4290 Molly Davis made changes -
                Status To-Do [ 10305 ] In Progress [ 3 ]
                Mdavis4290 Molly Davis made changes -
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                ann.loraine Ann Loraine made changes -
                Sprint Spring 4 [ 188 ] Spring 4, Spring 5 [ 188, 189 ]
                ann.loraine Ann Loraine made changes -
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                Mdavis4290 Molly Davis added a comment - - edited

                Flavonoid repo:

                Branch: https://bitbucket.org/mdavis4290/molly5-flavonoid-rnaseq/branch/IGBF-3627

                Show
                Mdavis4290 Molly Davis added a comment - - edited Flavonoid repo : Branch : https://bitbucket.org/mdavis4290/molly5-flavonoid-rnaseq/branch/IGBF-3627
                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 ]
                ann.loraine Ann Loraine made changes -
                Status Needs 1st Level Review [ 10005 ] First Level Review in Progress [ 10301 ]
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                ann.loraine Ann Loraine added a comment -

                Please modify sample sheet as follows:

                • Remove the first row (first row should be column names)
                • Change "study name" column values to "Muday pollen tube SRP460750"
                • Change "Display Name" values so that "cool" is replaced with "28C" and "warm" is replaced with "34C"
                • After "Treatment" column insert a new column with column name "temp". Insert values 28 or 34 for column values into this new column, according to the temperature the sample got.
                • Before "Treatment" column, insert a new column with column name "Genotype Details" and copy the values currently in "Genotype" to this new column.
                • In the current "Genotype" column, replace values currently there with abbreviated codes for each of the genotypes, using the same terminology as in our older sample sheet: 72_F3H_PollenTube/Documentation/muday-144_sample_sheet.xlsx (ARE instead of "anthocyanin reduced (are)" for example)
                Show
                ann.loraine Ann Loraine added a comment - Please modify sample sheet as follows: Remove the first row (first row should be column names) Change "study name" column values to "Muday pollen tube SRP460750" Change "Display Name" values so that "cool" is replaced with "28C" and "warm" is replaced with "34C" After "Treatment" column insert a new column with column name "temp". Insert values 28 or 34 for column values into this new column, according to the temperature the sample got. Before "Treatment" column, insert a new column with column name "Genotype Details" and copy the values currently in "Genotype" to this new column. In the current "Genotype" column, replace values currently there with abbreviated codes for each of the genotypes, using the same terminology as in our older sample sheet: 72_F3H_PollenTube/Documentation/muday-144_sample_sheet.xlsx (ARE instead of "anthocyanin reduced (are)" for example)
                ann.loraine Ann Loraine made changes -
                Assignee Ann Loraine [ aloraine ] Molly Davis [ molly ]
                ann.loraine Ann Loraine made changes -
                Status First Level Review in Progress [ 10301 ] To-Do [ 10305 ]
                Mdavis4290 Molly Davis made changes -
                Rank Ranked higher
                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-3627b
                PR: https://bitbucket.org/hotpollen/flavonoid-rnaseq/pull-requests/41

                Note: Changed the location of the file to Documentation where the older sample sheet is located.

                Show
                Mdavis4290 Molly Davis added a comment - Branch : https://bitbucket.org/mdavis4290/molly5-flavonoid-rnaseq/branch/IGBF-3627b PR : https://bitbucket.org/hotpollen/flavonoid-rnaseq/pull-requests/41 Note: Changed the location of the file to Documentation where the older sample sheet is located.
                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 -
                Status Needs 1st Level Review [ 10005 ] First Level Review in Progress [ 10301 ]
                Mdavis4290 Molly Davis made changes -
                Status First Level Review in Progress [ 10301 ] Ready for Pull Request [ 10304 ]
                Mdavis4290 Molly Davis made changes -
                Status Ready for Pull Request [ 10304 ] Pull Request Submitted [ 10101 ]
                Mdavis4290 Molly Davis made changes -
                Assignee Ann Loraine [ aloraine ]
                ann.loraine Ann Loraine made changes -
                Sprint Spring 4, Spring 5 [ 188, 189 ] Spring 4, Spring 5, Spring 6 [ 188, 189, 190 ]
                ann.loraine Ann Loraine made changes -
                Rank Ranked higher
                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 ]
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                ann.loraine Ann Loraine added a comment -

                Note:

                We need to double-check that the sample codes listed in the spreadsheet match the sample codes shown on the SRA Web pages for each record.

                Show
                ann.loraine Ann Loraine added a comment - Note: We need to double-check that the sample codes listed in the spreadsheet match the sample codes shown on the SRA Web pages for each record.
                ann.loraine Ann Loraine made changes -
                Sprint Spring 4, Spring 5, Spring 6 [ 188, 189, 190 ] Spring 4, Spring 5, Spring 6, Spring 7 [ 188, 189, 190, 191 ]
                ann.loraine Ann Loraine made changes -
                Rank Ranked higher
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                ann.loraine Ann Loraine added a comment -

                Molly noted during scrum that she gets the run names and sample codes via manual query at SRA to creates a "csv" file with the data. This becomes the beginning of the sample spreadsheet.

                To QA the sample code / SRR identifier mapping

                • she could repeat this process and add that csv file to the repository under "Documentation" folder.
                • she could write a markdown or are more simple script (python, bash) that compares the list of SRR/sample codes in the sample spreadsheet to what the SRA reports
                Show
                ann.loraine Ann Loraine added a comment - Molly noted during scrum that she gets the run names and sample codes via manual query at SRA to creates a "csv" file with the data. This becomes the beginning of the sample spreadsheet. To QA the sample code / SRR identifier mapping she could repeat this process and add that csv file to the repository under "Documentation" folder. she could write a markdown or are more simple script (python, bash) that compares the list of SRR/sample codes in the sample spreadsheet to what the SRA reports
                Hide
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                Mdavis4290 Molly Davis added a comment -

                Add that csv file to the repository under "Documentation" folder

                Branch: https://bitbucket.org/mdavis4290/molly5-flavonoid-rnaseq/branch/IGBF-3627c

                Show
                Mdavis4290 Molly Davis added a comment - Add that csv file to the repository under "Documentation" folder Branch: https://bitbucket.org/mdavis4290/molly5-flavonoid-rnaseq/branch/IGBF-3627c
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                ann.loraine Ann Loraine added a comment -

                Thank you Molly Davis! Please submit a PR for this new branch and then we can close off the ticket.

                Show
                ann.loraine Ann Loraine added a comment - Thank you Molly Davis ! Please submit a PR for this new branch and then we can close off the ticket.
                ann.loraine Ann Loraine made changes -
                Status Merged Needs Testing [ 10002 ] Post-merge Testing In Progress [ 10003 ]
                ann.loraine Ann Loraine made changes -
                Status Post-merge Testing In Progress [ 10003 ] To-Do [ 10305 ]
                ann.loraine Ann Loraine made changes -
                Status To-Do [ 10305 ] In Progress [ 3 ]
                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 -
                Assignee Ann Loraine [ aloraine ] Molly Davis [ molly ]
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                Mdavis4290 Molly Davis added a comment -

                PR: https://bitbucket.org/hotpollen/flavonoid-rnaseq/pull-requests/43

                Show
                Mdavis4290 Molly Davis added a comment - PR : https://bitbucket.org/hotpollen/flavonoid-rnaseq/pull-requests/43
                Mdavis4290 Molly Davis made changes -
                Status Ready for Pull Request [ 10304 ] Pull Request Submitted [ 10101 ]
                Mdavis4290 Molly Davis made changes -
                Assignee Molly Davis [ molly ] Ann Loraine [ aloraine ]
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                ann.loraine Ann Loraine added a comment -

                Merged! Closing the ticket.

                Show
                ann.loraine Ann Loraine added a comment - Merged! Closing the ticket.
                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 -
                Assignee Ann Loraine [ aloraine ] Molly Davis [ molly ]

                  People

                  • Assignee:
                    Mdavis4290 Molly Davis
                    Reporter:
                    Mdavis4290 Molly Davis
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                    Dates

                    • Created:
                      Updated:
                      Resolved: