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:1
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Epic Link:
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Sprint:Spring 8 2023 Apr 24
Description
Suggestions for improvement - to make the image look nicer:
Pick some pretty colors to distinguish protein-coding genes (e.g., KanR, F3H) from the other features. Currently, all the features have the same color (RGB code 0,0,255). If you do that, then we can make a very nice visualization by turning on the "Color by RGB" feature in the track.
Copy the values from field 14 into field 13.
You can curate field 14 a bit more, by judiciously copying over some of the text annotations from each feature in the original GenBank file.
Find the bed file in bitbucket: https://bitbucket.org/hotpollen/flavonoid-rnaseq/src/main/ExternalDataSets/pK7WG2-F3H-OX3.bed
Attachments
Issue Links
- relates to
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- Closed
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Activity
| Field | Original Value | New Value |
|---|---|---|
| Epic Link |
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| Link | This issue blocks IGBF-3306 [ IGBF-3306 ] |
| Assignee | Ann Loraine [ aloraine ] | Molly Davis [ molly ] |
| Description |
Suggestions for improvement - to make the image look nicer:
Pick some pretty colors to distinguish protein-coding genes (e.g., KanR, F3H) from the other features. Currently, all the features have the same color (RGB code 0,0,255). If you do that, then we can make a very nice visualization by turning on the "Color by RGB" feature in the track. Copy the values from field 14 into field 13. You can curate field 14 a bit more, by judiciously copying over some of the text annotations from each feature in the original GenBank file. Find the bed file in ticket IGBF-3306 |
Suggestions for improvement - to make the image look nicer:
Pick some pretty colors to distinguish protein-coding genes (e.g., KanR, F3H) from the other features. Currently, all the features have the same color (RGB code 0,0,255). If you do that, then we can make a very nice visualization by turning on the "Color by RGB" feature in the track. Copy the values from field 14 into field 13. You can curate field 14 a bit more, by judiciously copying over some of the text annotations from each feature in the original GenBank file. Find the bed file in bitbucket: https://bitbucket.org/mdavis4290/molly-flavonoid-rnaseq/src/main/ExternalDataSets/pK7WG2-F3H-OX3.bed |
| Description |
Suggestions for improvement - to make the image look nicer:
Pick some pretty colors to distinguish protein-coding genes (e.g., KanR, F3H) from the other features. Currently, all the features have the same color (RGB code 0,0,255). If you do that, then we can make a very nice visualization by turning on the "Color by RGB" feature in the track. Copy the values from field 14 into field 13. You can curate field 14 a bit more, by judiciously copying over some of the text annotations from each feature in the original GenBank file. Find the bed file in bitbucket: https://bitbucket.org/mdavis4290/molly-flavonoid-rnaseq/src/main/ExternalDataSets/pK7WG2-F3H-OX3.bed |
Suggestions for improvement - to make the image look nicer:
Pick some pretty colors to distinguish protein-coding genes (e.g., KanR, F3H) from the other features. Currently, all the features have the same color (RGB code 0,0,255). If you do that, then we can make a very nice visualization by turning on the "Color by RGB" feature in the track. Copy the values from field 14 into field 13. You can curate field 14 a bit more, by judiciously copying over some of the text annotations from each feature in the original GenBank file. Find the bed file in bitbucket: https://bitbucket.org/hotpollen/flavonoid-rnaseq/src/main/ExternalDataSets/pK7WG2-F3H-OX3.bed |
| Status | To-Do [ 10305 ] | In Progress [ 3 ] |
| Status | In Progress [ 3 ] | Needs 1st Level Review [ 10005 ] |
| Assignee | Molly Davis [ molly ] | Ann Loraine [ aloraine ] |
| 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 ] |
Getting BED file from branch via URL:
Functional Review:
- Opened the plasmid sequence as a new "Custom Genome"
- Opened plasmid bed file version 2 on topic branch
- Changed "Color by" parameter to "R,G,B" for the plasmid bed file track
- Made image - see attached
Could be improved. If we do that, we should do it in a separate ticket after closing this one.
- Title (field 13) could be better. This is what appears in the "Selection Info" box in the upper right corner when a user clicks on a thing.
- Id (field 4) for "ColE1/pMB1/..." should be shorter. Move some of this information to the "Description" (field 14)
- Things that come in pairs (e.g., LB and RB) should probably be the same color.
| Attachment | pK7WG-F3H-4.png [ 17859 ] |
Code is fine.
Please rebase topic branch on team repository's main branch. Pull request should update.
Moving to "ready for pull request". When branch is updated, please move to "pull request submitted" and un-assign it.
| Status | First Level Review in Progress [ 10301 ] | Ready for Pull Request [ 10304 ] |
| Assignee | Ann Loraine [ aloraine ] | Molly Davis [ molly ] |
Rebasing:
git checkout IGBF-3315 git rebase main git push --force origin IGBF-3315
Made a new pull request:
https://bitbucket.org/hotpollen/flavonoid-rnaseq/pull-requests/13
| Status | Ready for Pull Request [ 10304 ] | Pull Request Submitted [ 10101 ] |
| Assignee | Molly Davis [ molly ] | Ann Loraine [ aloraine ] |
| Status | Pull Request Submitted [ 10101 ] | Reviewing Pull Request [ 10303 ] |
| Status | Reviewing Pull Request [ 10303 ] | Merged Needs Testing [ 10002 ] |
Merged.
Moving DONE without any further testing.
| Status | Merged Needs Testing [ 10002 ] | Post-merge Testing In Progress [ 10003 ] |
| Resolution | Done [ 10000 ] | |
| Status | Post-merge Testing In Progress [ 10003 ] | Closed [ 6 ] |
| Assignee | Ann Loraine [ aloraine ] | Molly Davis [ molly ] |
Branch: https://bitbucket.org/mdavis4290/molly-flavonoid-rnaseq/branch/IGBF-3315
Review: