Details
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Type:
Task
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Status: Closed (View Workflow)
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Priority:
Major
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Resolution: Done
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Affects Version/s: None
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Fix Version/s: None
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Labels:None
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Story Points:2
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Epic Link:
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Sprint:Spring 4, Spring 5, Spring 6, Spring 7
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.
Attachments
Issue Links
Activity
| Field | Original Value | New Value |
|---|---|---|
| Epic Link | IGBF-2993 [ 21429 ] |
| Rank | Ranked higher |
| Status | To-Do [ 10305 ] | In Progress [ 3 ] |
| Rank | Ranked lower |
| Sprint | Spring 4 [ 188 ] | Spring 4, Spring 5 [ 188, 189 ] |
| Rank | Ranked higher |
| Assignee | Molly Davis [ molly ] |
| Status | In Progress [ 3 ] | Needs 1st Level Review [ 10005 ] |
| Assignee | Ann Loraine [ aloraine ] |
| Status | Needs 1st Level Review [ 10005 ] | First Level Review in Progress [ 10301 ] |
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)
| Assignee | Ann Loraine [ aloraine ] | Molly Davis [ molly ] |
| Status | First Level Review in Progress [ 10301 ] | To-Do [ 10305 ] |
| Rank | Ranked higher |
| Status | To-Do [ 10305 ] | In Progress [ 3 ] |
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.
| Assignee | Molly Davis [ molly ] |
| Status | In Progress [ 3 ] | Needs 1st Level Review [ 10005 ] |
| Status | Needs 1st Level Review [ 10005 ] | First Level Review in Progress [ 10301 ] |
| Status | First Level Review in Progress [ 10301 ] | Ready for Pull Request [ 10304 ] |
| Status | Ready for Pull Request [ 10304 ] | Pull Request Submitted [ 10101 ] |
| Assignee | Ann Loraine [ aloraine ] |
| Sprint | Spring 4, Spring 5 [ 188, 189 ] | Spring 4, Spring 5, Spring 6 [ 188, 189, 190 ] |
| Rank | Ranked higher |
| Status | Pull Request Submitted [ 10101 ] | Reviewing Pull Request [ 10303 ] |
| Status | Reviewing Pull Request [ 10303 ] | Merged Needs Testing [ 10002 ] |
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.
| Sprint | Spring 4, Spring 5, Spring 6 [ 188, 189, 190 ] | Spring 4, Spring 5, Spring 6, Spring 7 [ 188, 189, 190, 191 ] |
| Rank | Ranked higher |
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
Add that csv file to the repository under "Documentation" folder
Branch: https://bitbucket.org/mdavis4290/molly5-flavonoid-rnaseq/branch/IGBF-3627c
Thank you Molly Davis! Please submit a PR for this new branch and then we can close off the ticket.
| Status | Merged Needs Testing [ 10002 ] | Post-merge Testing In Progress [ 10003 ] |
| Status | Post-merge Testing In Progress [ 10003 ] | To-Do [ 10305 ] |
| Status | To-Do [ 10305 ] | In Progress [ 3 ] |
| Status | In Progress [ 3 ] | Needs 1st Level Review [ 10005 ] |
| Status | Needs 1st Level Review [ 10005 ] | First Level Review in Progress [ 10301 ] |
| Status | First Level Review in Progress [ 10301 ] | Ready for Pull Request [ 10304 ] |
| Assignee | Ann Loraine [ aloraine ] | Molly Davis [ molly ] |
| Status | Ready for Pull Request [ 10304 ] | Pull Request Submitted [ 10101 ] |
| Assignee | Molly Davis [ molly ] | Ann Loraine [ aloraine ] |
Merged! Closing the ticket.
| Status | Pull Request Submitted [ 10101 ] | Reviewing Pull Request [ 10303 ] |
| Status | Reviewing Pull Request [ 10303 ] | Merged Needs Testing [ 10002 ] |
| Status | Merged Needs Testing [ 10002 ] | Post-merge Testing In Progress [ 10003 ] |
| Resolution | Done [ 10000 ] | |
| Status | Post-merge Testing In Progress [ 10003 ] | Closed [ 6 ] |
| Assignee | Ann Loraine [ aloraine ] | Molly Davis [ molly ] |
Flavonoid repo:
Branch: https://bitbucket.org/mdavis4290/molly5-flavonoid-rnaseq/branch/IGBF-3627