Details
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Type:
Task
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Status: To-Do (View Workflow)
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Priority:
Major
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Resolution: Unresolved
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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:Spring 9 2023 May 1, Summer 2 2023 May 29
Description
Now that we have processed data from SRP371294 data, we need to make the processed data files available for visualization in IGB.
For this, we will make a sample spreadsheet named SRP371294_sample_sheet.xlsx and then use it as a new input to the script "makeAnnotsXml.py" residing in hotpollen repo "genome-browser-visualization" to enable users to view the data in IGB.
To do:
- Review existing sample sheets in "splicing analysis" repository in https://bitbucket.org/hotpollen/splicing-analysis/src/main/ExternalData/
- Create a new spreadsheet named SRP371294_sample_sheet.xlsx and fill in the columns using information from Sequence Read Archive records for SRP371294. Use the existing sample spreadsheets as a guide for how best to do this.
- Modify the script "makeAnnotsXml.py" in hotpollen repo "genome-browser-visualization" to include the new spreadsheet. Note that if you have errors in the spreadsheet, the script will likely fail. Also note that you will have modify the script to accommodate a new dataset that not tomato and that does not reside in the same physical location as the others.
- To check the annots.xml file and the resulting visualizations, following the instructions in the "README" file at https://bitbucket.org/hotpollen/genome-browser-visualization/src/main/
To Test:
- Check that every file can be loaded into IGB
- Visualize genes SR45A and SR30 to observe possible splicing differences between sample types.
Other relevant information:
- The physical location of the data files on our data deployment host is: http://lorainelab-quickload.scidas.org/rnaseq/A_thaliana_Jun_2009/SRP371294/
- Genome version for this data set is A_thaliana_Jun_2009
Attachments
Issue Links
Activity
| Field | Original Value | New Value |
|---|---|---|
| Epic Link | IGBF-2993 [ 21429 ] |
| Summary | Add SRP371294 to Quickload RNA-Seq annots.xml | Create SRP371294 spreadsheet for adding data to "hotpollen" annots.xml |
| Assignee | Ann Loraine [ aloraine ] |
| Description |
Now that we have processed data from SRP371294 data, we need to make the processed data files available for visualization in IGB.
For this, we will make a sample spreadsheet named SRP371294_sample_sheet.xlsx and then use it as a new input to the script "makeAnnotsXml.py" residing in hotpollen repo "genome-browser-visualization" to enable users to view the data in IGB. To do: * Review existing sample sheets in "splicing analysis" repository in https://bitbucket.org/hotpollen/splicing-analysis/src/main/ExternalData/ * Create a new spreadsheet named SRP371294_sample_sheet.xlsx and fill in the columns using information from Sequence Read Archive records for SRP371294 * Use files from https://bitbucket.org/hotpollen/splicing-analysis/src/main/ExternalData/ as a guide. Note how spreadsheets describing data harvested from SRA use SRA accessions for sample codes and different values in the URL column compared to data sets not taken from SRA. * Modify the script "makeAnnotsXml.py" to include the new spreadsheet. Note that if you have errors in the spreadsheet, the script will likely fail to run properly. Ask Loraine for physical file locations for this data set on the data deployment host. * To check the annots.xml file and the resulting visualizations, following the instructions in the "README" file at https://bitbucket.org/hotpollen/genome-browser-visualization/src/main/ To Test: * Check that every file can be loaded into IGB |
| Description |
Now that we have processed data from SRP371294 data, we need to make the processed data files available for visualization in IGB.
For this, we will make a sample spreadsheet named SRP371294_sample_sheet.xlsx and then use it as a new input to the script "makeAnnotsXml.py" residing in hotpollen repo "genome-browser-visualization" to enable users to view the data in IGB. To do: * Review existing sample sheets in "splicing analysis" repository in https://bitbucket.org/hotpollen/splicing-analysis/src/main/ExternalData/ * Create a new spreadsheet named SRP371294_sample_sheet.xlsx and fill in the columns using information from Sequence Read Archive records for SRP371294 * Use files from https://bitbucket.org/hotpollen/splicing-analysis/src/main/ExternalData/ as a guide. Note how spreadsheets describing data harvested from SRA use SRA accessions for sample codes and different values in the URL column compared to data sets not taken from SRA. * Modify the script "makeAnnotsXml.py" to include the new spreadsheet. Note that if you have errors in the spreadsheet, the script will likely fail to run properly. Ask Loraine for physical file locations for this data set on the data deployment host. * To check the annots.xml file and the resulting visualizations, following the instructions in the "README" file at https://bitbucket.org/hotpollen/genome-browser-visualization/src/main/ To Test: * Check that every file can be loaded into IGB |
Now that we have processed data from SRP371294 data, we need to make the processed data files available for visualization in IGB.
For this, we will make a sample spreadsheet named SRP371294_sample_sheet.xlsx and then use it as a new input to the script "makeAnnotsXml.py" residing in hotpollen repo "genome-browser-visualization" to enable users to view the data in IGB. To do: * Review existing sample sheets in "splicing analysis" repository in https://bitbucket.org/hotpollen/splicing-analysis/src/main/ExternalData/ * Create a new spreadsheet named SRP371294_sample_sheet.xlsx and fill in the columns using information from Sequence Read Archive records for SRP371294 * Use files from https://bitbucket.org/hotpollen/splicing-analysis/src/main/ExternalData/ as a guide. Note how spreadsheets describing data harvested from SRA use SRA accessions for sample codes and different values in the URL column compared to data sets not taken from SRA. * Modify the script "makeAnnotsXml.py" to include the new spreadsheet. Note that if you have errors in the spreadsheet, the script will likely fail to run properly. Ask Loraine for physical file locations for this data set on the data deployment host. * To check the annots.xml file and the resulting visualizations, following the instructions in the "README" file at https://bitbucket.org/hotpollen/genome-browser-visualization/src/main/ To Test: * Check that every file can be loaded into IGB * Visualize genes SR45A and SR30 to observe possible splicing differences between sample types. |
| Story Points | 0.5 | 2 |
| Summary | Create SRP371294 spreadsheet for adding data to "hotpollen" annots.xml | Create SRP371294 and test spreadsheet for adding data to "hotpollen" annots.xml |
| Description |
Now that we have processed data from SRP371294 data, we need to make the processed data files available for visualization in IGB.
For this, we will make a sample spreadsheet named SRP371294_sample_sheet.xlsx and then use it as a new input to the script "makeAnnotsXml.py" residing in hotpollen repo "genome-browser-visualization" to enable users to view the data in IGB. To do: * Review existing sample sheets in "splicing analysis" repository in https://bitbucket.org/hotpollen/splicing-analysis/src/main/ExternalData/ * Create a new spreadsheet named SRP371294_sample_sheet.xlsx and fill in the columns using information from Sequence Read Archive records for SRP371294 * Use files from https://bitbucket.org/hotpollen/splicing-analysis/src/main/ExternalData/ as a guide. Note how spreadsheets describing data harvested from SRA use SRA accessions for sample codes and different values in the URL column compared to data sets not taken from SRA. * Modify the script "makeAnnotsXml.py" to include the new spreadsheet. Note that if you have errors in the spreadsheet, the script will likely fail to run properly. Ask Loraine for physical file locations for this data set on the data deployment host. * To check the annots.xml file and the resulting visualizations, following the instructions in the "README" file at https://bitbucket.org/hotpollen/genome-browser-visualization/src/main/ To Test: * Check that every file can be loaded into IGB * Visualize genes SR45A and SR30 to observe possible splicing differences between sample types. |
Now that we have processed data from SRP371294 data, we need to make the processed data files available for visualization in IGB.
For this, we will make a sample spreadsheet named SRP371294_sample_sheet.xlsx and then use it as a new input to the script "makeAnnotsXml.py" residing in hotpollen repo "genome-browser-visualization" to enable users to view the data in IGB. To do: * Review existing sample sheets in "splicing analysis" repository in https://bitbucket.org/hotpollen/splicing-analysis/src/main/ExternalData/ * Create a new spreadsheet named SRP371294_sample_sheet.xlsx and fill in the columns using information from Sequence Read Archive records for SRP371294. Use the existing sample spreadsheets as a guide for how best to do this. * Modify the script "makeAnnotsXml.py" in hotpollen repo "genome-browser-visualization" to include the new spreadsheet. Note that if you have errors in the spreadsheet, the script will likely fail. Also note that you will have modify the script to accommodate a new dataset that not tomato and that does not reside in the same physical location as the others. * To check the annots.xml file and the resulting visualizations, following the instructions in the "README" file at https://bitbucket.org/hotpollen/genome-browser-visualization/src/main/ To Test: * Check that every file can be loaded into IGB * Visualize genes SR45A and SR30 to observe possible splicing differences between sample types. Other relevant information: * The physical location of the data files on our data deployment host is: http://lorainelab-quickload.scidas.org/rnaseq/A_thaliana_Jun_2009/SRP371294/ * Genome version for this data set is A_thaliana_Jun_2009 |
| Description |
Now that we have processed data from SRP371294 data, we need to make the processed data files available for visualization in IGB.
For this, we will make a sample spreadsheet named SRP371294_sample_sheet.xlsx and then use it as a new input to the script "makeAnnotsXml.py" residing in hotpollen repo "genome-browser-visualization" to enable users to view the data in IGB. To do: * Review existing sample sheets in "splicing analysis" repository in https://bitbucket.org/hotpollen/splicing-analysis/src/main/ExternalData/ * Create a new spreadsheet named SRP371294_sample_sheet.xlsx and fill in the columns using information from Sequence Read Archive records for SRP371294. Use the existing sample spreadsheets as a guide for how best to do this. * Modify the script "makeAnnotsXml.py" in hotpollen repo "genome-browser-visualization" to include the new spreadsheet. Note that if you have errors in the spreadsheet, the script will likely fail. Also note that you will have modify the script to accommodate a new dataset that not tomato and that does not reside in the same physical location as the others. * To check the annots.xml file and the resulting visualizations, following the instructions in the "README" file at https://bitbucket.org/hotpollen/genome-browser-visualization/src/main/ To Test: * Check that every file can be loaded into IGB * Visualize genes SR45A and SR30 to observe possible splicing differences between sample types. Other relevant information: * The physical location of the data files on our data deployment host is: http://lorainelab-quickload.scidas.org/rnaseq/A_thaliana_Jun_2009/SRP371294/ * Genome version for this data set is A_thaliana_Jun_2009 |
Now that we have processed data from SRP371294 data, we need to make the processed data files available for visualization in IGB.
For this, we will make a sample spreadsheet named SRP371294_sample_sheet.xlsx and then use it as a new input to the script "makeAnnotsXml.py" residing in hotpollen repo "genome-browser-visualization" to enable users to view the data in IGB. To do: * Review existing sample sheets in "splicing analysis" repository in https://bitbucket.org/hotpollen/splicing-analysis/src/main/ExternalData/ * Create a new spreadsheet named SRP371294_sample_sheet.xlsx and fill in the columns using information from Sequence Read Archive records for SRP371294. Use the existing sample spreadsheets as a guide for how best to do this. * Modify the script "makeAnnotsXml.py" in hotpollen repo "genome-browser-visualization" to include the new spreadsheet. Note that if you have errors in the spreadsheet, the script will likely fail. Also note that you will have modify the script to accommodate a new dataset that not tomato and that does not reside in the same physical location as the others. * To check the annots.xml file and the resulting visualizations, following the instructions in the "README" file at https://bitbucket.org/hotpollen/genome-browser-visualization/src/main/ To Test: * Check that every file can be loaded into IGB * Visualize genes SR45A and SR30 to observe possible splicing differences between sample types. Other relevant information: * The physical location of the data files on our data deployment host is: http://lorainelab-quickload.scidas.org/rnaseq/A_thaliana_Jun_2009/SRP371294/ * Genome version for this data set is A_thaliana_Jun_2009 |
| Rank | Ranked higher |
| Summary | Create SRP371294 and test spreadsheet for adding data to "hotpollen" annots.xml | Create and test SRP371294 sample sheet spreadsheet for adding data to "hotpollen" annots.xml |
| Status | To-Do [ 10305 ] | In Progress [ 3 ] |
| Assignee | Molly Davis [ molly ] |
| Attachment | SRP371294_sample_sheet.xlsx [ 17878 ] |
| Status | In Progress [ 3 ] | Needs 1st Level Review [ 10005 ] |
| Assignee | Molly Davis [ molly ] |
| Status | Needs 1st Level Review [ 10005 ] | First Level Review in Progress [ 10301 ] |
| Status | First Level Review in Progress [ 10301 ] | To-Do [ 10305 ] |
| Assignee | Molly Davis [ molly ] |
| Status | To-Do [ 10305 ] | In Progress [ 3 ] |
| Attachment | SRP371294_sample_sheet.xlsx [ 17878 ] |
| Comment |
[ Draft 1 sample sheet:
[^SRP371294_sample_sheet.xlsx] ] |
| Attachment | SRP371294_sample_sheet.xlsx [ 17879 ] |
| Status | In Progress [ 3 ] | Needs 1st Level Review [ 10005 ] |
| Assignee | Molly Davis [ molly ] |
| Sprint | Spring 9 2023 May 1 [ 169 ] | Spring 9 2023 May 1, Summer 1 2023 May 15 [ 169, 170 ] |
| Rank | Ranked higher |
| Status | Needs 1st Level Review [ 10005 ] | First Level Review in Progress [ 10301 ] |
| Status | First Level Review in Progress [ 10301 ] | To-Do [ 10305 ] |
| Assignee | Molly Davis [ molly ] |
| 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 ] |
| Assignee | Molly Davis [ molly ] |
| Status | Pull Request Submitted [ 10101 ] | Reviewing Pull Request [ 10303 ] |
| Status | Reviewing Pull Request [ 10303 ] | To-Do [ 10305 ] |
| Assignee | Molly Davis [ molly ] |
| Sprint | Spring 9 2023 May 1, Summer 1 2023 May 15 [ 169, 170 ] | Spring 9 2023 May 1, Summer 2 2023 May 29 [ 169, 171 ] |
| Assignee | Molly Davis [ molly ] |
| Sprint | Spring 9 2023 May 1, Summer 2 2023 May 29 [ 169, 171 ] | Spring 9 2023 May 1, Summer 2 2023 May 29, Summer 3 2023 June 12 [ 169, 171, 172 ] |
| Rank | Ranked higher |
| Sprint | Spring 9 2023 May 1, Summer 2 2023 May 29, Summer 3 2023 June 12 [ 169, 171, 172 ] | Spring 9 2023 May 1, Summer 2 2023 May 29, Summer 4 2023 June 26 [ 169, 171, 173 ] |
| Sprint | Spring 9 2023 May 1, Summer 2 2023 May 29, Summer 4 2023 June 26 [ 169, 171, 173 ] | Spring 9 2023 May 1, Summer 2 2023 May 29 [ 169, 171 ] |
| Rank | Ranked higher |