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:Summer 7 2023 Aug 7, Fall 2 2023 Sep 17, Fall 3 2023 Oct 2
Description
Refer to ticket IGBF-3423 to locate SRA data.
SRP460750
For this task, we need to confirm and sanity-check the Muday time course data that Rob uploaded and submitted to the Sequence Read Archive.
If the data are good, we will replace all the existing BAM, junctions, etc. files deployed in the "hotpollen" quickload site with newly processed data.
For this task:
- Check SRP on NCBI and review submission
- Download the data onto the cluster by using the SRP name
- Run nf-core/rnaseq pipeline
- Run our coverage graph and junctions scripts on the data
Note that all files should now use their "SRR" names instead of the existing file names.
Attachments
Issue Links
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Activity
| Field | Original Value | New Value |
|---|---|---|
| Epic Link | IGBF-2993 [ 21429 ] |
| Status | To-Do [ 10305 ] | In Progress [ 3 ] |
| Status | In Progress [ 3 ] | To-Do [ 10305 ] |
| Status | To-Do [ 10305 ] | In Progress [ 3 ] |
| Sprint | Summer 7 2023 Aug 7 [ 176 ] | Summer 7 2023 Aug 7, Summer 8 2023 Aug 21 [ 176, 177 ] |
| Rank | Ranked higher |
| Status | In Progress [ 3 ] | To-Do [ 10305 ] |
| Assignee | Molly Davis [ molly ] |
| Sprint | Summer 7 2023 Aug 7, Summer 8 2023 Aug 21 [ 176, 177 ] | Testing 2 : 4 Nov - 15 Nov, Summer 7 2023 Aug 7 [ 82, 176 ] |
| Sprint | Fall 1 - Sep 5, Summer 7 2023 Aug 7 [ 82, 176 ] | Summer 7 2023 Aug 7, Fall 2 2023 Sep 17 [ 176, 178 ] |
| Rank | Ranked lower |
| Summary | Re-run Nextflow Muday time course data with new SRA submission | Re-run Nextflow Muday time course data with data downloaded from SRA |
| Rank | Ranked lower |
| Assignee | Molly Davis [ molly ] |
| Status | To-Do [ 10305 ] | In Progress [ 3 ] |
| Sprint | Summer 7 2023 Aug 7, Fall 2 2023 Sep 17 [ 176, 178 ] | Summer 7 2023 Aug 7, Fall 2 2023 Sep 17, Fall 3 2023 Oct 2 [ 176, 178, 179 ] |
| Rank | Ranked higher |
| Status | In Progress [ 3 ] | To-Do [ 10305 ] |
| Status | To-Do [ 10305 ] | In Progress [ 3 ] |
| Assignee | Molly Davis [ molly ] |
| Status | In Progress [ 3 ] | Needs 1st Level Review [ 10005 ] |
| Assignee | Ann Loraine [ aloraine ] |
| Assignee | Ann Loraine [ aloraine ] | Robert Reid [ robertreid ] |
| Status | Needs 1st Level Review [ 10005 ] | First Level Review in Progress [ 10301 ] |
| Assignee | Robert Reid [ robertreid ] | Molly Davis [ molly ] |
| Comment | [ *Branch*: https://bitbucket.org/mdavis4290/molly3-flavonoid-rnaseq/branch/IGBF-3406 ] |
| Assignee | Molly Davis [ molly ] | Ann Loraine [ aloraine ] |
| Status | First Level Review in Progress [ 10301 ] | Needs 1st Level Review [ 10005 ] |
| Assignee | Ann Loraine [ aloraine ] |
| Status | Needs 1st Level Review [ 10005 ] | First Level Review in Progress [ 10301 ] |
| Status | First Level Review in Progress [ 10301 ] | Ready for Pull Request [ 10304 ] |
| Assignee | Molly Davis [ molly ] |
| 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 ] |
| Description |
Refer to ticket SRP460750 |
Refer to ticket SRP460750 For this task, we need to confirm and sanity-check the Muday time course data that Rob uploaded and submitted to the Sequence Read Archive. If the data are good, we will replace all the existing BAM, junctions, etc. files deployed in the "hotpollen" quickload site with newly processed data. For this task: * Check SRP on NCBI and review submission * Download the data onto the cluster by using the SRP name * Run nf-core/rnaseq pipeline * Run our coverage graph and junctions scripts on the data Note that all files should now use their "SRR" names instead of the existing file names. |
| Summary | Re-run Nextflow Muday time course data with data downloaded from SRA | Re-run Nextflow Muday time course data with SL5 data downloaded from SRA |