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 1 - Sep 5, Summer 8 2023 Aug 21, Fall 2 2023 Sep 17, Fall 3 2023 Oct 2
Description
My apologies if this has already been done and I lost track of the data somehow!
For this task, we need to align and deploy data from Azenta run 30-804059537 onto the SL4 / S_lycopersicum_Sep_2019 genome, using the S_lycopersicum_Sep_2019 assembly and accompanying gene annotations.
To-do:
- run the nextflow pipeline as per usual. Please use location /projects/tomato_genome/fnb/dataprocessing/30-804059537-KP/S_lycopersicum_Sep_2019 on the UNCC cluster
- create a branch in the code repo as usual
- commit to the branch the following files:
30-804059537_SL4_multiqc_report.html (renamed from multiqc_report.html)
30-804059537_SL4_salmon.merged.gene_counts.tsv (renamed from salmon.merged.gene_counts.tsv)
- create coverage graphs and junction files, as per usual
- move just the coverage graphs, bam files, and junction files to this location: /projects/tomato_genome/fnb/dataprocessing/30-804059537-KP/for_quickload/S_lycopersicum_Sep_2019/30-804059537 (We'll use this as the source directory for an rsync command that will copy these data over the data.bioviz.org host for visualization in IGB)
Attachments
Issue Links
- relates to
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- Closed
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Activity
| Field | Original Value | New Value |
|---|---|---|
| Epic Link | IGBF-3251 [ 22132 ] |
| Sprint | Summer 8 2023 Aug 21 [ 177 ] | |
| Assignee | Ann Loraine [ aloraine ] |
| Summary | Process 30-804059537 (KP 2023) data to S_lycopersicum_Sep_2019 (SL4) genome | Process 30-804059537 (KP 2023) data using S_lycopersicum_Sep_2019 (SL4) genome |
| Summary | Process 30-804059537 (KP 2023) data using S_lycopersicum_Sep_2019 (SL4) genome | Process 30-804059537 (KP 2023) data using S_lycopersicum_Sep_2019 (SL4) genome assembly and annotations |
| Assignee | Molly Davis [ molly ] |
| Status | To-Do [ 10305 ] | In Progress [ 3 ] |
| Assignee | Molly Davis [ molly ] |
| Status | In Progress [ 3 ] | Needs 1st Level Review [ 10005 ] |
| Assignee | Robert Reid [ robertreid ] |
| Status | Needs 1st Level Review [ 10005 ] | First Level Review in Progress [ 10301 ] |
| Status | First Level Review in Progress [ 10301 ] | To-Do [ 10305 ] |
| Assignee | Robert Reid [ robertreid ] | Molly Davis [ molly ] |
| Status | To-Do [ 10305 ] | In Progress [ 3 ] |
| Sprint | Summer 8 2023 Aug 21 [ 177 ] | Testing 2 : 4 Nov - 15 Nov, Summer 8 2023 Aug 21 [ 82, 177 ] |
| Rank | Ranked higher |
| Comment | [ I believe the reference .fa file is having issues on the cluster. After being moved they possibly could have been corrupted. I am going to wget the reference genome files from online if cp the file from the direct location on the cluster does not work. ] |
| 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 ] |
| Comment | [ Next step: decide next step as part of review. ] |
| Status | Needs 1st Level Review [ 10005 ] | First Level Review in Progress [ 10301 ] |
| Status | First Level Review in Progress [ 10301 ] | To-Do [ 10305 ] |
| Attachment | Unmapped Reads-Too short.pdf [ 17952 ] |
| Attachment | Unmapped Reads-Too short.pdf [ 17952 ] |
| Attachment | Unmapped-Reads.png [ 17953 ] |
| Status | To-Do [ 10305 ] | In Progress [ 3 ] |
| Status | In Progress [ 3 ] | Needs 1st Level Review [ 10005 ] |
| Assignee | Robert Reid [ robertreid ] |
| Sprint | Fall 1 - Sep 5, Summer 8 2023 Aug 21 [ 82, 177 ] | Fall 1 - Sep 5, Summer 8 2023 Aug 21, Fall 2 2023 Sep 17 [ 82, 177, 178 ] |
| Rank | Ranked higher |
| Status | Needs 1st Level Review [ 10005 ] | First Level Review in Progress [ 10301 ] |
| Assignee | Robert Reid [ robertreid ] |
| Status | First Level Review in Progress [ 10301 ] | Ready for Pull Request [ 10304 ] |
| Assignee | Molly Davis [ molly ] |
| Assignee | Molly Davis [ molly ] |
| Status | Ready for Pull Request [ 10304 ] | Pull Request Submitted [ 10101 ] |
| 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 ] |
| 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 ] |
| Assignee | Molly Davis [ molly ] |
| Resolution | Done [ 10000 ] | |
| Status | Closed [ 6 ] | To-Do [ 10305 ] |
| Sprint | Fall 1 - Sep 5, Summer 8 2023 Aug 21, Fall 2 2023 Sep 17 [ 82, 177, 178 ] | Fall 1 - Sep 5, Summer 8 2023 Aug 21, Fall 2 2023 Sep 17, Fall 3 2023 Oct 2 [ 82, 177, 178, 179 ] |
| Rank | Ranked higher |
| Assignee | Molly Davis [ molly ] |
| Status | To-Do [ 10305 ] | In Progress [ 3 ] |
| Status | In Progress [ 3 ] | To-Do [ 10305 ] |
| Assignee | Molly Davis [ molly ] |
| Status | To-Do [ 10305 ] | In Progress [ 3 ] |
| Status | In Progress [ 3 ] | Needs 1st Level Review [ 10005 ] |
| Assignee | Ann Loraine [ aloraine ] |
| Assignee | Ann Loraine [ aloraine ] |
| Assignee | Robert Reid [ robertreid ] |
| Status | Needs 1st Level Review [ 10005 ] | First Level Review in Progress [ 10301 ] |
| Assignee | Robert Reid [ robertreid ] | Molly Davis [ molly ] |
| 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 ] |
| Assignee | Ann Loraine [ aloraine ] |
| 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 ] |
| Assignee | Ann Loraine [ aloraine ] | Molly Davis [ molly ] |
| Link | This issue relates to IGBF-4347 [ IGBF-4347 ] |
| Link | This issue relates to IGBF-4347 [ IGBF-4347 ] |