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:3
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Epic Link:
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Sprint:Fall 6, Fall 7, Spring 1
Description
Re-run mark 2022 timeseries data with the name SRP441343 from SRA for both SL4 and SL5 genomes.
For this task, we need to confirm and sanity-check the mark 2022 time series 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
Activity
| Field | Original Value | New Value |
|---|---|---|
| Epic Link | IGBF-2993 [ 21429 ] |
| Rank | Ranked higher |
| Assignee | Molly Davis [ molly ] |
| Status | To-Do [ 10305 ] | In Progress [ 3 ] |
| Description | SRP441343 | Re-run mark 2022 timeseries data with the name SRP441343 from SRA for both SL4 and SL5 genomes. |
| Sprint | Fall 6 [ 182 ] | Fall 6, Fall 7 [ 182, 183 ] |
| Rank | Ranked higher |
| Assignee | Molly Davis [ molly ] |
| Status | In Progress [ 3 ] | Needs 1st Level Review [ 10005 ] |
| Assignee | Robert Reid [ robertreid ] |
| Description | Re-run mark 2022 timeseries data with the name SRP441343 from SRA for both SL4 and SL5 genomes. |
Re-run mark 2022 timeseries data with the name SRP441343 from SRA for both SL4 and SL5 genomes.
For this task, we need to confirm and sanity-check the mark 2022 time series 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. |
| 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 | Robert Reid [ robertreid ] | Molly Davis [ molly ] |
| Assignee | Molly Davis [ molly ] |
| Status | Ready for Pull Request [ 10304 ] | Pull Request Submitted [ 10101 ] |
| Sprint | Fall 6, Fall 7 [ 182, 183 ] | Fall 6, Fall 7, Fall 8 [ 182, 183, 184 ] |
| Rank | Ranked higher |
| Assignee | Ann Loraine [ aloraine ] |
| Status | Pull Request Submitted [ 10101 ] | Reviewing Pull Request [ 10303 ] |
| Status | Reviewing Pull Request [ 10303 ] | Merged Needs Testing [ 10002 ] |
| Assignee | Ann Loraine [ aloraine ] |
| Sprint | Fall 6, Fall 7, Fall 8 [ 182, 183, 184 ] | Fall 6, Fall 7, Spring 2 [ 182, 183, 186 ] |
| Sprint | Fall 6, Fall 7, Spring 2 [ 182, 183, 186 ] | Fall 6, Fall 7, Spring 1 [ 182, 183, 185 ] |
| Assignee | Molly Davis [ molly ] |
| Status | Merged Needs Testing [ 10002 ] | Post-merge Testing In Progress [ 10003 ] |
| Resolution | Done [ 10000 ] | |
| Status | Post-merge Testing In Progress [ 10003 ] | Closed [ 6 ] |