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:Summer 1, Summer 2, Summer 3
Description
GOAL: To identify all APX gene locations in SL4 genome using the GFF file.
Search through the GFF file (SL4 version, ITAG 4.0) for each instance of ascorbate peroxidase.
We are looking for lines that are "genes" and not exons, etc. Need to genome coordinates
Chromosome #, start position and stop position.
Make a summary of all of these and save to a file.
Attachments
Activity
| Field | Original Value | New Value |
|---|---|---|
| Epic Link | IGBF-2993 [ 21429 ] |
| Status | To-Do [ 10305 ] | In Progress [ 3 ] |
Here are the chromosomes that I found:
https://docs.google.com/spreadsheets/d/1Fes2tuad0hVGBUKESWXlRHsfsb1ZZ1WAnvnv7xycCiM/edit?usp=sharing
| Status | In Progress [ 3 ] | Needs 1st Level Review [ 10005 ] |
Scale the Y-axis to all be the same.
| Sprint | Summer 1 [ 218 ] | Summer 1, Summer 2 [ 218, 219 ] |
| Rank | Ranked higher |
| Status | Needs 1st Level Review [ 10005 ] | First Level Review in Progress [ 10301 ] |
| Status | First Level Review in Progress [ 10301 ] | 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 ] |
| Status | Pull Request Submitted [ 10101 ] | Reviewing Pull Request [ 10303 ] |
| Status | Reviewing Pull Request [ 10303 ] | To-Do [ 10305 ] |
| Status | To-Do [ 10305 ] | In Progress [ 3 ] |
| Sprint | Summer 1, Summer 2 [ 218, 219 ] | Summer 1, Summer 2, Summer 3 [ 218, 219, 220 ] |
| Rank | Ranked higher |
| 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 ] |
| 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 ] |
The GFF file is needed to get the coords.
https://drive.google.com/file/d/17VrqLTWJiUe644fHVrjWy2-BWZUj7epv/view?usp=drive_link
Find each "gene" that is ascorbate peroxidase. Get coords, the chromosme and start and stop positions.