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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:
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          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

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                Mdavis4290 Molly Davis added a comment - - edited

                Flavonoid repo:

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

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                Mdavis4290 Molly Davis added a comment - - edited Flavonoid repo : Branch : https://bitbucket.org/mdavis4290/molly5-flavonoid-rnaseq/branch/IGBF-3627
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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)
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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.
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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.
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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
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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.

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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.
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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
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                ann.loraine Ann Loraine added a comment -

                Merged! Closing the ticket.

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                ann.loraine Ann Loraine added a comment - Merged! Closing the ticket.

                  People

                  • Assignee:
                    Mdavis4290 Molly Davis
                    Reporter:
                    Mdavis4290 Molly Davis
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                    • Created:
                      Updated:
                      Resolved: