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:0.5
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Epic Link:
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Sprint:Summer 2 2023 May 29, Summer 3 2023 June 12, Summer 4 2023 June 26, Summer 5 2023 July 10, Summer 6 2023 July 24
Description
Now that our pollen and seedling data are submitted to SRA, we are planning to download and re-run our nf-core rnaseq pipeline on the data as it exists in the SRA. Then, we will deploy the newly re-run data to IGB Quickload for users to view and explore. To re-deploy the data we need a new sample sheet that uses SRA names instead of our project-specific names.
For this task, create a new sample spreadsheet named for the project name which uses the new SRA names.
See the linked ticket IGBF-3254 for a mapping between original fastq file names and new SRA names.
Attachments
Issue Links
- relates to
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- Closed
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Activity
| Field | Original Value | New Value |
|---|---|---|
| Epic Link | IGBF-2993 [ 21429 ] |
| Link | This issue relates to IGBF-3347 [ IGBF-3347 ] |
| Rank | Ranked higher |
| Sprint | Summer 2 2023 May 29 [ 171 ] | Summer 2 2023 May 29, Summer 3 2023 June 12 [ 171, 172 ] |
| Rank | Ranked higher |
| Assignee | Molly Davis [ molly ] |
| Status | To-Do [ 10305 ] | In Progress [ 3 ] |
| Attachment | seedlingPollen_sample_sheet.xlsx [ 17902 ] |
| Assignee | Molly Davis [ molly ] |
| Status | In Progress [ 3 ] | Needs 1st Level Review [ 10005 ] |
| Attachment | seedlingPollen_sample_sheet.xlsx [ 17902 ] |
| Attachment | seedlingPollen_sample_sheet.xlsx [ 17903 ] |
| Attachment | seedlingPollen_sample_sheet.xlsx [ 17903 ] |
| Status | Needs 1st Level Review [ 10005 ] | First Level Review in Progress [ 10301 ] |
| Assignee | Ann Loraine [ aloraine ] |
add 3 columns (after the existing ones):
- replicate (1, 2, or 3)
- temperature in degrees C (37 or 28)
- tissue ("mature pollen" or "seedling")
change existing columns as follows:
- Replace values in "Study Name" and "Physical Folder" to the "SRP" accession: SRP438952
- Replace values in "Sample URL" with https://www.ncbi.nlm.nih.gov/sra
- Replace values in "Sample code" with the "SRR" values for each row
- Change values in "treatment" with "heat stress" or "control"
- Change display name values to "[genotype] [tissue] [temperature] [treatment] [replicate]" e.g, "Heinz seedling 37 heat stress 1"
| Status | First Level Review in Progress [ 10301 ] | To-Do [ 10305 ] |
| Assignee | Ann Loraine [ aloraine ] |
| Sprint | Summer 2 2023 May 29, Summer 3 2023 June 12 [ 171, 172 ] | Summer 2 2023 May 29, Summer 3 2023 June 12, Summer 4 2023 June 26 [ 171, 172, 173 ] |
| Rank | Ranked higher |
| Assignee | Molly Davis [ molly ] |
| Status | To-Do [ 10305 ] | In Progress [ 3 ] |
| Status | In Progress [ 3 ] | To-Do [ 10305 ] |
| Status | To-Do [ 10305 ] | In Progress [ 3 ] |
Version 2 Updated Sample Sheet:
Branch: https://bitbucket.org/mdavis4290/molly-splicing-analysis/branch/IGBF-3348b
| Status | In Progress [ 3 ] | Needs 1st Level Review [ 10005 ] |
| Assignee | Molly Davis [ molly ] | Ann Loraine [ aloraine ] |
| Assignee | Ann Loraine [ aloraine ] |
| Assignee | Ann Loraine [ aloraine ] |
| Status | Needs 1st Level Review [ 10005 ] | First Level Review in Progress [ 10301 ] |
| Status | First Level Review in Progress [ 10301 ] | Needs 1st Level Review [ 10005 ] |
| Sprint | Summer 2 2023 May 29, Summer 3 2023 June 12, Summer 4 2023 June 26 [ 171, 172, 173 ] | Summer 2 2023 May 29, Summer 3 2023 June 12, Summer 4 2023 June 26, Summer 5 2023 July 10 [ 171, 172, 173, 174 ] |
| Rank | Ranked higher |
| Status | Needs 1st Level Review [ 10005 ] | First Level Review in Progress [ 10301 ] |
Visited folder https://bitbucket.org/mdavis4290/molly-splicing-analysis/src/IGBF-3348b/ExternalData/ and downloaded proposed new sample sheet, file name: SRP438952_sample_sheet.xlsx.
Change request(s):
1) Column "Physical folder" contains nonsensical values. For example, the first three rows are: SRP438952, SRP438953, and SRP438954.
2) This is a minor issue, but I noticed that some values in column "Color" contain hash characters (#) and others do not. The downstream code (makeAnnotsXml.py and others) can handle both, I think. A hash character is probably good to include as this would make it super-clear that the values are hexadecimal color codes. But I have no preference either way.
I did not proof-read every row; instead, I mainly just scanned over the values. Apart from the preceding issues, the data are fine.
For future commits, it sure would be nice if [~molly] could preserve the "freeze top row" formatting. Freezing that top row really helps a lot when interacting with this spreadsheet! It's very nice to have that top row, the row that contains the column names, always stay in view when scrolling through the data.
| Status | First Level Review in Progress [ 10301 ] | To-Do [ 10305 ] |
| Assignee | Ann Loraine [ aloraine ] | Molly Davis [ molly ] |
| Status | To-Do [ 10305 ] | In Progress [ 3 ] |
Version 3 of Updated Sample Sheet:
Branch: https://bitbucket.org/mdavis4290/molly-splicing-analysis/branch/IGBF-3348c
| Status | In Progress [ 3 ] | Needs 1st Level Review [ 10005 ] |
| Assignee | Molly Davis [ molly ] |
| Assignee | Ann Loraine [ aloraine ] |
| Status | Needs 1st Level Review [ 10005 ] | First Level Review in Progress [ 10301 ] |
Testing:
- I fetched the new branch from [~molly]'s repository
- I opened the new version of the Excel-format spreadsheet
- I observed that the "SRP" numbers in column "Study Name" and "Physical Folder" now are all "SRP438952" as requested
- I observed that the header is now frozen - it remains stationary when I scroll up and down the spreadsheet
Based on the above observations, I recommend that the branch be merged into "main" as usual.
| Status | First Level Review in Progress [ 10301 ] | Ready for Pull Request [ 10304 ] |
| Assignee | Ann Loraine [ aloraine ] | Molly Davis [ molly ] |
| Sprint | Summer 2 2023 May 29, Summer 3 2023 June 12, Summer 4 2023 June 26, Summer 5 2023 July 10 [ 171, 172, 173, 174 ] | Summer 2 2023 May 29, Summer 3 2023 June 12, Summer 4 2023 June 26, Summer 5 2023 July 10, Summer 6 2023 July 24 [ 171, 172, 173, 174, 175 ] |
| Rank | Ranked higher |
| Status | Ready for Pull Request [ 10304 ] | Pull Request Submitted [ 10101 ] |
| Assignee | Molly Davis [ molly ] | Ann Loraine [ aloraine ] |
| 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 ] |
Version 1 Sample Sheet:
Branch: https://bitbucket.org/mdavis4290/molly-splicing-analysis/branch/IGBF-3348