Details
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Type:
Task
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Status: Closed (View Workflow)
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Priority:
Minor
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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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Epic Link:
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Sprint:Spring 4, Spring 5
Description
This task is more of a brainstorm based on the details that came out of Kelsey's committee meeting.
In her meeting, an advisor inquired about how Heinz is the reference genome and a sample in the experiment. It would make sense that Heinz will more easily align to reference genome compared to the other 3 TMH varieties.
The PCA (attached) reflects this.
The goal would be to come up with an unbiased way to check MDS / PCA / PCoA where everything is not aligned to Heinz.
1 idea.
- We de novo assembly via trinity.
- Get a set of genes for each variety.
- Assign all of these genes to a SolyID via blast. Along with a gene expression count.
- Run these as a MDS / PCA and see the distribution.
Attachments
Activity
| Field | Original Value | New Value |
|---|---|---|
| Epic Link | IGBF-2993 [ 21429 ] |
| Sprint | Spring 5 [ 189 ] | Spring 4 [ 188 ] |
| Rank | Ranked lower |
| Status | To-Do [ 10305 ] | In Progress [ 3 ] |
| Sprint | Spring 4 [ 188 ] | Spring 4, Spring 5 [ 188, 189 ] |
| 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 ] |