Details
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Type:
Organization Issue
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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 9, Spring 10
Description
Situation: I was attempting to add several coverage graph tracks from the "PT time GM lab" folder in the RNA-Seq Quickload when I encountered a "Cannot add same feature" error. The track I was trying to add was titled "A.28.75.8 cool ARE pollen tube 75 min scaled coverage" but the error shows that that track points to a different data file than what it's titled ("8-are-75-min-34C.scaled.bedgraph.gz", see attached).
I took a look through the SL5 annots.xml file and have found that all of the .8 and .9 replicates from the Muday study have incorrect titles (see attached). I only pulled out lines from annots.xml that pertained to coverage graphs to create the attached spreadsheet, but please note that ALL file types (.bam, .bedgraph.gz, and .bed.gz) have this mislabeling issue with these replicates.
Task: Correct the title field in the SL5 annots.xml file for all .8 and .9 replicates from the Muday study.
Attachments
Issue Links
- relates to
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IGBF-3711 Set up SRA-downloaded Muday datasets in the RNA-Seq Quickload
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- Closed
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Activity
| Field | Original Value | New Value |
|---|---|---|
| Epic Link | IGBF-2993 [ 21429 ] |
| Description |
Situation: I was attempting to add several coverage graph tracks from the "PT time GM lab" folder in the RNA-Seq Quickload when I encountered a "Cannot add same feature" error. The track I was trying to add was titled "A.28.75.8 cool ARE pollen tube 75 min scaled coverage" but the error shows that that track points to a different data file than what it's titled ("8-are-75-min-34C.scaled.bedgraph.gz", see attached).
I took a look through the SL5 annots.xml file and have found that all of the .8 and .9 replicates have incorrect titles (see attached). I only pulled out lines from annots.xml that pertained to coverage graphs to create the attached spreadsheet, but please note that *ALL* file types (.bam, .bedgraph.gz, and .bed.gz) have this mislabeling issue with these replicates. Task: Correct the title field in the SL5 annots.xml file for all .8 and .9 replicates. |
Situation: I was attempting to add several coverage graph tracks from the "PT time GM lab" folder in the RNA-Seq Quickload when I encountered a "Cannot add same feature" error. The track I was trying to add was titled "A.28.75.8 cool ARE pollen tube 75 min scaled coverage" but the error shows that that track points to a different data file than what it's titled ("8-are-75-min-34C.scaled.bedgraph.gz", see attached).
I took a look through the SL5 annots.xml file and have found that all of the .8 and .9 replicates from the Muday study have incorrect titles (see attached). I only pulled out lines from annots.xml that pertained to coverage graphs to create the attached spreadsheet, but please note that *ALL* file types (.bam, .bedgraph.gz, and .bed.gz) have this mislabeling issue with these replicates. Task: Correct the title field in the SL5 annots.xml file for all .8 and .9 replicates from the Muday study. |
| Assignee | Ann Loraine [ aloraine ] |
| 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 ] |
| Assignee | Ann Loraine [ aloraine ] |
Attention: Paige Kulzer
Please test and make sure the issue you identified is no longer a problem.
| Assignee | Paige Kulzer [ pkulzer ] |
| Sprint | Spring 9 [ 193 ] | Spring 9, Spring 10 [ 193, 194 ] |
| Rank | Ranked higher |
| Status | Merged Needs Testing [ 10002 ] | Post-merge Testing In Progress [ 10003 ] |
All scaled coverage graph replicates are now able to be loaded without error. Moving to done.
| Resolution | Done [ 10000 ] | |
| Status | Post-merge Testing In Progress [ 10003 ] | Closed [ 6 ] |
| Assignee | Paige Kulzer [ pkulzer ] | Ann Loraine [ aloraine ] |
I fixed the code that makes the annots.xml files and redeployed the Quickload site.
For review, see: