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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Sprint:Fall 4 2023 Oct 16, Fall 5
Description
The goal is to add to the existing EB-SEQ table results (From IBGF-3454).
The table currently includes the EB-SEQ results along with the SolyID and gene description.
What we can add:
- The read expression counts data from Salmon.
- The deseq2 results, values, log fold changes, pvalues, etc.
- EdgeR data
This would produce an unwieldy table, 100's of columns long!
I am going to first touch base with Gloria about what would be the most useful.
Attachments
Issue Links
- is blocked by
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- Closed
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Activity
| Field | Original Value | New Value |
|---|---|---|
| Epic Link | IGBF-2993 [ 21429 ] |
| Description |
The goal is to add to the existing EB-SEQ table results (From IBGF-3454). The table currently includes the EB-SEQ results along with the SolyID and gene description. What we can add: * The read expression counts data from Salmon. * The deseq2 results, values, log fold changes, pvalues, etc. * EdgeR data This would produce an unwieldy table, 100's of columns long! I am going to first touch base with Gloria about what would be the most useful. |
The goal is to add to the existing EB-SEQ table results (From IBGF-3454).
The table currently includes the EB-SEQ results along with the SolyID and gene description. What we can add: * The read expression counts data from Salmon. * The deseq2 results, values, log fold changes, pvalues, etc. * EdgeR data This would produce an unwieldy table, 100's of columns long! I am going to first touch base with Gloria about what would be the most useful. |
| Sprint | Fall 4 2023 Oct 16 [ 180 ] |
| Sprint | Fall 4 2023 Oct 16 [ 180 ] | Fall 4 2023 Oct 16, Fall 5 [ 180, 181 ] |
| Rank | Ranked higher |
| Status | To-Do [ 10305 ] | In Progress [ 3 ] |
| Status | In Progress [ 3 ] | To-Do [ 10305 ] |
| Status | To-Do [ 10305 ] | In Progress [ 3 ] |
| 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 ] |
Until we hear back from Gloria's group that they plan to harness this analysis in some way, we will close this task.
When they ask for this again along with more related data, we can open a new ticket at that time.
Did not get to chat with Gloria in Wake Forest. She was juggling 50 things!
What might look cool in this table would be the MvW results that Ann produced comparing are versus VF36 and recently shared with Gloria's lab.
Table I refer to is in bitbucket here:
https://bitbucket.org/hotpollen/flavonoid-rnaseq/src/main/72_F3H_PollenTube/results/MvW-SL4.txt
We have the following comparisons:
awk '
{ print $2 "\t" $3 }' MvW-SL4.txt | sort | uniq
Each of these sets could be added as columns to the EBSEQ table. I am thinking of adding just the LOGFOLD change result for each set.
Or maybe the P-value also. This would be 9 expts X 2 results for 18 more columns!
Still manageable I think.
Sounds like a Python script!