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:3
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Epic Link:
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Sprint:Summer 3, Summer 4, Summer 5
Description
Turns out we have genomic data for Tamaulipas.
Produced in 2022, we downloaded the data to the HPC, summarized the sequence numbers.
And never touched it again.
We need to get it in to the SRA! Asap because it was used in Sorel's paper.
The data is located here along with the Azenta info.
https://drive.google.com/drive/folders/1lBL07t9ea5NL8h-bOve5Qj3yG2xpt2MU?usp=drive_link
The azenta id for this run is: 30-693209853
The actual data is backed up in the following folder:
/projects/tomato_genome/genome/30-693209853/00_fastq
In here there are 3 types of files:
- Tam
- CHM34
- CHM22
First I will email Mark and get clarification of what CHM22 and CHM34 are.
And then start the data gathering.
Attachments
Activity
| Field | Original Value | New Value |
|---|---|---|
| Epic Link | IGBF-2993 [ 21429 ] |
| Status | To-Do [ 10305 ] | In Progress [ 3 ] |
Going to assign this to Brandon.
Take a look at the Google folder and the 2 files within.
You are looking for typos and errors.
| Assignee | Robert Reid [ robertreid ] | Brandon Bendickson [ bbendick ] |
| Sprint | Summer 3 [ 197 ] | Summer 3, Summer 4 [ 197, 198 ] |
| Rank | Ranked higher |
| Status | In Progress [ 3 ] | Needs 1st Level Review [ 10005 ] |
| Sprint | Summer 3, Summer 4 [ 197, 198 ] | Summer 3, Summer 4, Summer 5 [ 197, 198, 199 ] |
| Rank | Ranked higher |
| 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 ] |
| 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 ] |
This appears complete and done and submitted.
Mark responded.
There is a single set of data that is Tamaulipas, with the other sequences being arabidopsis.
Making a folder to hold the Biosample and SRA metadata for submission here:
https://drive.google.com/drive/folders/1g-PbRBkbYlJ6kaeventqOvYO4vhfidyT?usp=drive_link
This is about as simple as a submission can get.