Details
-
Type:
Task
-
Status: Closed (View Workflow)
-
Priority:
Major
-
Resolution: Done
-
Affects Version/s: None
-
Fix Version/s: None
-
Labels:None
-
Story Points:3
-
Epic Link:
-
Sprint:Summer 5 2022 July 18, Summer 6 2022 Aug 1, Fall 6 2022 Nov 7
Description
This is needed to deploy the new data files for visualization in IGB.
Attachments
Issue Links
- is blocked by
-
-
- Closed
-
-
-
- Closed
-
-
-
- Closed
-
- relates to
-
-
- Closed
-
Activity
| Field | Original Value | New Value |
|---|---|---|
| Epic Link | IGBF-2993 [ 21429 ] |
| Description |
* Run code to generate scaled coverage graphs (ask Ann for details)
* Run code to generate function files (ask Ann for details) * Generate annots.xml files for IGB Quickload for visualization (ask Ann for details) |
* Run code to generate scaled coverage graphs (ask Ann for details)
* Run code to generate junctions files (ask Ann for details) * Generate annots.xml files for IGB Quickload for visualization (ask Ann for details) |
| Story Points | 2 | 3 |
| Sprint | Summer 5 2022 July 18 [ 151 ] | Summer 5 2022 July 18, Summer 6 2022 Aug 1 [ 151, 152 ] |
| Rank | Ranked higher |
| Sprint | Summer 5 2022 July 18, Summer 6 2022 Aug 1 [ 151, 152 ] | Summer 5 2022 July 18, Summer 6 2022 Aug 1, Fall 1 2022 Aug 15 [ 151, 152, 153 ] |
| Rank | Ranked higher |
| Description |
* Run code to generate scaled coverage graphs (ask Ann for details)
* Run code to generate junctions files (ask Ann for details) * Generate annots.xml files for IGB Quickload for visualization (ask Ann for details) |
* Run code to generate scaled coverage graphs - see https://bitbucket.org/hotpollen/flavonoid-rnaseq/src/c53c3b94da5a/src/bamCoverage.sh
* Run code to generate junctions files (ask Ann for details) * Generate annots.xml files for IGB Quickload for visualization (ask Ann for details) |
| Summary | Run post-processing on alt splicing RNA-Seq samples | Make annots.xml for RNA-Seq junction, alignment, and coverage graphs |
| Description |
* Run code to generate scaled coverage graphs - see https://bitbucket.org/hotpollen/flavonoid-rnaseq/src/c53c3b94da5a/src/bamCoverage.sh
* Run code to generate junctions files (ask Ann for details) * Generate annots.xml files for IGB Quickload for visualization (ask Ann for details) |
| Description | This is needed to deploy the new data files for visualization in IGB. |
| Link | This issue is blocked by IGBF-3161 [ IGBF-3161 ] |
| Sprint | Summer 5 2022 July 18, Summer 6 2022 Aug 1, Fall 1 2022 Aug 15 [ 151, 152, 153 ] | Summer 5 2022 July 18, Summer 6 2022 Aug 1, Fall 2 2022 Sep 5 [ 151, 152, 154 ] |
| Status | To-Do [ 10305 ] | In Progress [ 3 ] |
| Status | In Progress [ 3 ] | To-Do [ 10305 ] |
| Status | To-Do [ 10305 ] | In Progress [ 3 ] |
Copied annots.xml generating code from flavonoid-rnaseq/src to splicing-analysis/src. Need to update the code with new sample names.
| Assignee | Ann Loraine [ aloraine ] |
Copying data to renci host. Started a tmux sessions and then did:
[aloraine@str-i1 star_salmon]$ pwd /nobackup/tomato_genome/alt_splicing/SRP252265/results/star_salmon [aloraine@str-i1 star_salmon]$ scp -o 'ProxyJump aloraine@hop.renci.org' *.bam.bai aloraine@lorainelab-quickload.scidas.org:/projects/igbquickload/lorainelab/www/main/htdocs/hotpollen/S_lycopersicum_Jun_2022/data/. [aloraine@str-i1 star_salmon]$ scp -o 'ProxyJump aloraine@hop.renci.org' *.bam aloraine@lorainelab-quickload.scidas.org:/projects/igbquickload/lorainelab/www/main/htdocs/hotpollen/S_lycopersicum_Jun_2022/data/.
| Sprint | Summer 5 2022 July 18, Summer 6 2022 Aug 1, Fall 2 2022 Sep 5 [ 151, 152, 154 ] | Summer 5 2022 July 18, Summer 6 2022 Aug 1 [ 151, 152 ] |
| Status | In Progress [ 3 ] | To-Do [ 10305 ] |
| Assignee | Ann Loraine [ aloraine ] |
| Sprint | Summer 5 2022 July 18, Summer 6 2022 Aug 1 [ 151, 152 ] | Summer 5 2022 July 18, Summer 6 2022 Aug 1, Fall 6 2022 Nov 7 [ 151, 152, 158 ] |
| Assignee | Ann Loraine [ aloraine ] |
| Status | To-Do [ 10305 ] | In Progress [ 3 ] |
| Status | In Progress [ 3 ] | To-Do [ 10305 ] |
| Status | To-Do [ 10305 ] | In Progress [ 3 ] |
Working on branch https://bitbucket.org/aloraine/splicing-analysis/branch/IGBF-3144
| Attachment | screenshot-1.png [ 17566 ] |
makeAnnotsXml.py creates quickload directory structure with meta-data files, including annots.xml.
However, the display folder structure has a bug - only one subfolder named 
is made.
| 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 ] |
Fixed above bug.
Quickload site is written to subdirectory "quickload" inside ManageQuickload folder. Using fully qualified file name in file tags. Files are deployed to renci host http://lorainelab-quickload.scidas.org/hotpollen/S_lycopersicum_Jun_2022/[ srp accession number ]/[ file name]
Checked that could load a few files in IGB. Made some png files on first chromosome.
To review that the data files were made correctly, we need to look at them in IGB. So, for this, I need to create the annots.xml files and add them to a Quickload site.