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:Winter 1, Spring 1
Description
GOAL: Given that we now have bam files and salmon count tables for each of the 4 tomato varieties, we can run Deseq2 on these tables and look at some relative comparisons within a variety.
We can't compare across varieties. No common gene connections since this is de novo results.
- Find one of Molly's recent deseq scripts to use as a template if not already having one.
- Pull each of the 4 gene counts tables.
- Run each one and we can look at volcano plots, PCA, etc
NEXTFLOW and Salmon produce many salmon count tables. I am guessing that this one:
salmon.merged.gene_counts.tsv
would be a good file to use. We don't TPM because deseq will take care of that.
And we don't need transcript level.
Attachments
Activity
| Field | Original Value | New Value |
|---|---|---|
| Epic Link | IGBF-2993 [ 21429 ] |
| Assignee | Ann Loraine [ aloraine ] | Robert Reid [ robertreid ] |
| Assignee | Robert Reid [ robertreid ] | Brandon Bendickson [ bbendick ] |
| Status | To-Do [ 10305 ] | In Progress [ 3 ] |
| Sprint | Winter 1 [ 209 ] | Winter 1, Spring 1 [ 209, 210 ] |
| 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 ] |