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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Epic Link:
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Sprint:Fall 6, Spring 1, Spring 2, Spring 3, Spring 9, Summer 1, Summer 2, Summer 3, Summer 4, Summer 5, Summer 6, Summer 7, Fall 1
Description
Directory: /projects/tomato_genome/fnb/dataprocessing
Review the SRA re-runs on the cluster for Muday, Johnson, mature pollen, and Ravi lab data. Once bam, junction, and coverage graph files have been produced and checked deploy data to IGB Quickload hotpollen host.
NOTE: This ticket changed in scope and focus a bit! The new goal is:
- Complete comparative evaluation of pre- and post-submission RNA-Seq data using multiqc results and special code written for this purpose.
This goal builds on the final work that Molly Davis did for us, before her appointment ended. We need to complete this work this sprint because we need to recover the large amount of disk space used up by running nf-core/rnaseq pipeline.
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Show 3 more links (3 relates to)
Activity
| Field | Original Value | New Value |
|---|---|---|
| Epic Link | IGBF-2993 [ 21429 ] |
| Description | Review the SRA re-runs on the cluster for Muday, Johnson, mature pollen, and Ravi lab data. Once bam, junction, and coverage graph files have been produced and checked deploy data to IGB Quickload host. | Review the SRA re-runs on the cluster for Muday, Johnson, mature pollen, and Ravi lab data. Once bam, junction, and coverage graph files have been produced and checked deploy data to IGB Quickload hotpollen host. |
| Sprint | Fall 6 [ 182 ] | Fall 6, Fall 7 [ 182, 183 ] |
| Rank | Ranked higher |
| Summary | Review SRA Re-runs | Review SRA Re-runs and submit to Quickload |
| Description | Review the SRA re-runs on the cluster for Muday, Johnson, mature pollen, and Ravi lab data. Once bam, junction, and coverage graph files have been produced and checked deploy data to IGB Quickload hotpollen host. |
*Directory*: /projects/tomato_genome/fnb/dataprocessing
Review the SRA re-runs on the cluster for Muday, Johnson, mature pollen, and Ravi lab data. Once bam, junction, and coverage graph files have been produced and checked deploy data to IGB Quickload hotpollen host. |
| Sprint | Fall 6, Fall 7 [ 182, 183 ] | Fall 6 [ 182 ] |
| Sprint | Fall 6 [ 182 ] | Fall 6, Spring 1 [ 182, 185 ] |
| Assignee | Molly Davis [ molly ] |
| Sprint | Fall 6, Spring 1 [ 182, 185 ] | Fall 6, Spring 1, Spring 2 [ 182, 185, 186 ] |
| Rank | Ranked higher |
| Sprint | Fall 6, Spring 1, Spring 2 [ 182, 185, 186 ] | Fall 6, Spring 1 [ 182, 185 ] |
| Sprint | Fall 6, Spring 1 [ 182, 185 ] | Fall 6, Spring 1, Spring 2 [ 182, 185, 186 ] |
| Summary | Review SRA Re-runs and submit to Quickload | Create spreadsheet to prepare to submit SRA Re-runs to Quickload |
| Rank | Ranked higher |
| Status | To-Do [ 10305 ] | In Progress [ 3 ] |
| Sprint | Fall 6, Spring 1, Spring 2 [ 182, 185, 186 ] | Fall 6, Spring 1, Spring 2, Spring 3 [ 182, 185, 186, 187 ] |
| Rank | Ranked higher |
| Status | In Progress [ 3 ] | To-Do [ 10305 ] |
| Rank | Ranked higher |
| Sprint | Fall 6, Spring 1, Spring 2, Spring 3 [ 182, 185, 186, 187 ] | Fall 6, Spring 1, Spring 2, Spring 3, Spring 4 [ 182, 185, 186, 187, 188 ] |
| Rank | Ranked higher |
| Sprint | Fall 6, Spring 1, Spring 2, Spring 3, Spring 4 [ 182, 185, 186, 187, 188 ] | Fall 6, Spring 1, Spring 2, Spring 3 [ 182, 185, 186, 187 ] |
| Sprint | Fall 6, Spring 1, Spring 2, Spring 3 [ 182, 185, 186, 187 ] | Fall 6, Spring 1, Spring 2, Spring 3, Spring 9 [ 182, 185, 186, 187, 193 ] |
| Rank | Ranked higher |
| Status | To-Do [ 10305 ] | In Progress [ 3 ] |
| Sprint | Fall 6, Spring 1, Spring 2, Spring 3, Spring 9 [ 182, 185, 186, 187, 193 ] | Fall 6, Spring 1, Spring 2, Spring 3, Spring 9, Spring 10 [ 182, 185, 186, 187, 193, 194 ] |
| Rank | Ranked higher |
| Status | In Progress [ 3 ] | To-Do [ 10305 ] |
| Status | To-Do [ 10305 ] | In Progress [ 3 ] |
| Status | In Progress [ 3 ] | To-Do [ 10305 ] |
| Sprint | Fall 6, Spring 1, Spring 2, Spring 3, Spring 9, Spring 10 [ 182, 185, 186, 187, 193, 194 ] | Fall 6, Spring 1, Spring 2, Spring 3, Spring 9, Summer 1 [ 182, 185, 186, 187, 193, 195 ] |
| Rank | Ranked higher |
| Sprint | Fall 6, Spring 1, Spring 2, Spring 3, Spring 9, Summer 1 [ 182, 185, 186, 187, 193, 195 ] | Fall 6, Spring 1, Spring 2, Spring 3, Spring 9, Summer 1, Summer 2 [ 182, 185, 186, 187, 193, 195, 196 ] |
| Rank | Ranked higher |
| Status | To-Do [ 10305 ] | In Progress [ 3 ] |
| Assignee | Molly Davis [ molly ] |
| Status | In Progress [ 3 ] | To-Do [ 10305 ] |
| Sprint | Fall 6, Spring 1, Spring 2, Spring 3, Spring 9, Summer 1, Summer 2 [ 182, 185, 186, 187, 193, 195, 196 ] | Fall 6, Spring 1, Spring 2, Spring 3, Spring 9, Summer 1, Summer 2, Summer 3 [ 182, 185, 186, 187, 193, 195, 196, 197 ] |
| Rank | Ranked higher |
| Sprint | Fall 6, Spring 1, Spring 2, Spring 3, Spring 9, Summer 1, Summer 2, Summer 3 [ 182, 185, 186, 187, 193, 195, 196, 197 ] | Fall 6, Spring 1, Spring 2, Spring 3, Spring 9, Summer 1, Summer 2, Summer 3, Summer 4 [ 182, 185, 186, 187, 193, 195, 196, 197, 198 ] |
| Rank | Ranked higher |
| Sprint | Fall 6, Spring 1, Spring 2, Spring 3, Spring 9, Summer 1, Summer 2, Summer 3, Summer 4 [ 182, 185, 186, 187, 193, 195, 196, 197, 198 ] | Fall 6, Spring 1, Spring 2, Spring 3, Spring 9, Summer 1, Summer 2, Summer 3, Summer 4, Summer 5 [ 182, 185, 186, 187, 193, 195, 196, 197, 198, 199 ] |
| Rank | Ranked higher |
| Sprint | Fall 6, Spring 1, Spring 2, Spring 3, Spring 9, Summer 1, Summer 2, Summer 3, Summer 4, Summer 5 [ 182, 185, 186, 187, 193, 195, 196, 197, 198, 199 ] | Fall 6, Spring 1, Spring 2, Spring 3, Spring 9, Summer 1, Summer 2, Summer 3, Summer 4, Summer 5, Summer 6 [ 182, 185, 186, 187, 193, 195, 196, 197, 198, 199, 200 ] |
| Rank | Ranked higher |
| Sprint | Fall 6, Spring 1, Spring 2, Spring 3, Spring 9, Summer 1, Summer 2, Summer 3, Summer 4, Summer 5, Summer 6 [ 182, 185, 186, 187, 193, 195, 196, 197, 198, 199, 200 ] | Fall 6, Spring 1, Spring 2, Spring 3, Spring 9, Summer 1, Summer 2, Summer 3, Summer 4, Summer 5, Summer 6, Summer 7 [ 182, 185, 186, 187, 193, 195, 196, 197, 198, 199, 200, 201 ] |
| Rank | Ranked higher |
| Summary | Create spreadsheet to prepare to submit SRA Re-runs to Quickload | Update data processing status by data set - by Molly |
| Summary | Update data processing status by data set - by Molly | Complete evaluation of RNA-Seq dataset submissions - are they okay? |
| Description |
*Directory*: /projects/tomato_genome/fnb/dataprocessing
Review the SRA re-runs on the cluster for Muday, Johnson, mature pollen, and Ravi lab data. Once bam, junction, and coverage graph files have been produced and checked deploy data to IGB Quickload hotpollen host. |
*Directory*: /projects/tomato_genome/fnb/dataprocessing
Review the SRA re-runs on the cluster for Muday, Johnson, mature pollen, and Ravi lab data. Once bam, junction, and coverage graph files have been produced and checked deploy data to IGB Quickload hotpollen host. NOTE: This ticket changed in scope and focus a bit! The new goal is: * Complete comparative evaluation of pre- and post-submission RNA-Seq data using multiqc results and special code written for this purpose. |
| Description |
*Directory*: /projects/tomato_genome/fnb/dataprocessing
Review the SRA re-runs on the cluster for Muday, Johnson, mature pollen, and Ravi lab data. Once bam, junction, and coverage graph files have been produced and checked deploy data to IGB Quickload hotpollen host. NOTE: This ticket changed in scope and focus a bit! The new goal is: * Complete comparative evaluation of pre- and post-submission RNA-Seq data using multiqc results and special code written for this purpose. |
*Directory*: /projects/tomato_genome/fnb/dataprocessing
Review the SRA re-runs on the cluster for Muday, Johnson, mature pollen, and Ravi lab data. Once bam, junction, and coverage graph files have been produced and checked deploy data to IGB Quickload hotpollen host. *NOTE*: This ticket changed in scope and focus a bit! The new goal is: * Complete comparative evaluation of pre- and post-submission RNA-Seq data using multiqc results and special code written for this purpose. This goal builds on the final work that [~Mdavis4290] did for us, before her appointment ended. We need to complete this work *this* sprint because we need to recover the large amount of disk space used up by running nf-core/rnaseq pipeline. |
| Summary | Complete evaluation of RNA-Seq dataset submissions - are they okay? | Complete evaluation of RNA-Seq dataset submissions - are you okay? |
| Status | To-Do [ 10305 ] | In Progress [ 3 ] |
| Assignee | Ann Loraine [ aloraine ] |
| Sprint | Fall 6, Spring 1, Spring 2, Spring 3, Spring 9, Summer 1, Summer 2, Summer 3, Summer 4, Summer 5, Summer 6, Summer 7 [ 182, 185, 186, 187, 193, 195, 196, 197, 198, 199, 200, 201 ] | Fall 6, Spring 1, Spring 2, Spring 3, Spring 9, Summer 1, Summer 2, Summer 3, Summer 4, Summer 5, Summer 6, Summer 7, Fall 1 [ 182, 185, 186, 187, 193, 195, 196, 197, 198, 199, 200, 201, 202 ] |
| Rank | Ranked higher |
| Status | In Progress [ 3 ] | To-Do [ 10305 ] |
| Status | To-Do [ 10305 ] | In Progress [ 3 ] |
| Summary | Complete evaluation of RNA-Seq dataset submissions - are you okay? | Complete evaluation of RNA-Seq dataset submissions |
| Comment |
[ To test:
Visit the RNA-Seq folder for both SL4 and SL5 genome versions - the two latest tomato assemblies. For each dataset shown in the RNA-Seq / PGRP, try to load a track for each of the checkboxes in each of the subfolders. If you see an error message stating that the data cannot be loaded, make a note of it. If all the datasets can be loaded into a track, please close this ticket. ] |
| 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 ] |
| Assignee | Brandon Bendickson [ bbendick ] |
| Status | Merged Needs Testing [ 10002 ] | Post-merge Testing In Progress [ 10003 ] |
| Status | Post-merge Testing In Progress [ 10003 ] | 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 ] |
| Status | Post-merge Testing In Progress [ 10003 ] | Merged Needs Testing [ 10002 ] |
| Status | Merged Needs Testing [ 10002 ] | Post-merge Testing In Progress [ 10003 ] |
| Status | Post-merge Testing In Progress [ 10003 ] | 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 ] |