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:0.25
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Epic Link:
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Sprint:Summer 5 2022 July 18, Summer 6 2022 Aug 1, Fall 1 2022 Aug 15, Fall 2 2022 Sep 5, Fall 3 2022 Sep 26, Fall 4 2022 Oct 10, Fall 5 2022 Oct 24, Fall 6 2022 Nov 7
Description
Git repository for this sub-project: https://bitbucket.org/hotpollen/splicing-analysis/src/master/
Use gene mapping table to add gene descriptions to new annotations bed-detail file for SL5.0 genome assembly release and annotations.
Specifically:
- Get the BED-detail gene model file from IGBQuickload repository: http://lorainelab-quickload.scidas.org/quickload/S_lycopersicum_Jun_2022/S_lycopersicum_Jun_2022.bed.gz
The 13th column of this file contains a gene identifier. The 4th column contains a transcript identifier. The final (14th) column contains "NA" for "Not Available." We would like it to instead contain a description of the gene. Since we don't have that, we would like to insert the description of gene counterparts present in the SL4.0 annotations.
- Note that the SL4 annotations can be found here: http://lorainelab-quickload.scidas.org/quickload/S_lycopersicum_Sep_2019/S_lycopersicum_Sep_2019.bed.gz
To map genes from SL4 onto SL5, you need a mapping file. The people who made SL5.0 gave us that mapping file back in July 2022:
Dear Ann,
Yes, we do have tables for the conversion between different versions. They are now avaiable on our website (http://solomics.agis.org.cn/tomato/ftp/ID_convert/).
Thanks so much for the intergration! I would be happy to forward it to my colleagues when it is avaiable.
Best regards,
Yao
Mapping files needed are also available in: /nobackup/tomato_genome/alt_splicing/mappingfiles
Attachments
Issue Links
Activity
| Field | Original Value | New Value |
|---|---|---|
| Epic Link | IGBF-2993 [ 21429 ] |
| Sprint | Summer 5 2022 July 18 [ 151 ] | Summer 5 2022 July 18, Summer 6 2022 Aug 1 [ 151, 152 ] |
| Rank | Ranked higher |
| Rank | Ranked higher |
| Description | Use gene mapping table to add gene descriptions to new annotations bed-detail file for SL5.0 genome assembly release and annotations. |
Use gene mapping table to add gene descriptions to new annotations bed-detail file for SL5.0 genome assembly release and annotations.
Specifically: * Get the BED-detail gene model file from IGBQuickload repository: http://lorainelab-quickload.scidas.org/quickload/S_lycopersicum_Jun_2022/S_lycopersicum_Jun_2022.bed.gz The 13th column of this file contains a gene identifier. The 4th column contains a transcript identifier. The final (14th) column contains "NA" for "Not Available." We would like it to instead contain a description of the gene. Since we don't have that, we would like to insert the description of gene counterparts present in the SL4.0 annotations. Note that the SL4 annotations can be found here: http://lorainelab-quickload.scidas.org/quickload/S_lycopersicum_Sep_2019/S_lycopersicum_Sep_2019.bed.gz |
| Description |
Use gene mapping table to add gene descriptions to new annotations bed-detail file for SL5.0 genome assembly release and annotations.
Specifically: * Get the BED-detail gene model file from IGBQuickload repository: http://lorainelab-quickload.scidas.org/quickload/S_lycopersicum_Jun_2022/S_lycopersicum_Jun_2022.bed.gz The 13th column of this file contains a gene identifier. The 4th column contains a transcript identifier. The final (14th) column contains "NA" for "Not Available." We would like it to instead contain a description of the gene. Since we don't have that, we would like to insert the description of gene counterparts present in the SL4.0 annotations. Note that the SL4 annotations can be found here: http://lorainelab-quickload.scidas.org/quickload/S_lycopersicum_Sep_2019/S_lycopersicum_Sep_2019.bed.gz |
Use gene mapping table to add gene descriptions to new annotations bed-detail file for SL5.0 genome assembly release and annotations.
Specifically: * Get the BED-detail gene model file from IGBQuickload repository: http://lorainelab-quickload.scidas.org/quickload/S_lycopersicum_Jun_2022/S_lycopersicum_Jun_2022.bed.gz The 13th column of this file contains a gene identifier. The 4th column contains a transcript identifier. The final (14th) column contains "NA" for "Not Available." We would like it to instead contain a description of the gene. Since we don't have that, we would like to insert the description of gene counterparts present in the SL4.0 annotations. * Note that the SL4 annotations can be found here: http://lorainelab-quickload.scidas.org/quickload/S_lycopersicum_Sep_2019/S_lycopersicum_Sep_2019.bed.gz To map genes from SL4 onto SL5, you need a mapping file. The people who made SL5.0 gave us that mapping file. |
| Description |
Use gene mapping table to add gene descriptions to new annotations bed-detail file for SL5.0 genome assembly release and annotations.
Specifically: * Get the BED-detail gene model file from IGBQuickload repository: http://lorainelab-quickload.scidas.org/quickload/S_lycopersicum_Jun_2022/S_lycopersicum_Jun_2022.bed.gz The 13th column of this file contains a gene identifier. The 4th column contains a transcript identifier. The final (14th) column contains "NA" for "Not Available." We would like it to instead contain a description of the gene. Since we don't have that, we would like to insert the description of gene counterparts present in the SL4.0 annotations. * Note that the SL4 annotations can be found here: http://lorainelab-quickload.scidas.org/quickload/S_lycopersicum_Sep_2019/S_lycopersicum_Sep_2019.bed.gz To map genes from SL4 onto SL5, you need a mapping file. The people who made SL5.0 gave us that mapping file. |
Use gene mapping table to add gene descriptions to new annotations bed-detail file for SL5.0 genome assembly release and annotations.
Specifically: * Get the BED-detail gene model file from IGBQuickload repository: http://lorainelab-quickload.scidas.org/quickload/S_lycopersicum_Jun_2022/S_lycopersicum_Jun_2022.bed.gz The 13th column of this file contains a gene identifier. The 4th column contains a transcript identifier. The final (14th) column contains "NA" for "Not Available." We would like it to instead contain a description of the gene. Since we don't have that, we would like to insert the description of gene counterparts present in the SL4.0 annotations. * Note that the SL4 annotations can be found here: http://lorainelab-quickload.scidas.org/quickload/S_lycopersicum_Sep_2019/S_lycopersicum_Sep_2019.bed.gz To map genes from SL4 onto SL5, you need a mapping file. The people who made SL5.0 gave us that mapping file. Author Yao me this: {quote} Dear Ann, Yes, we do have tables for the conversion between different versions. They are now avaiable on our website (http://solomics.agis.org.cn/tomato/ftp/ID_convert/). Thanks so much for the intergration! I would be happy to forward it to my colleagues when it is avaiable. Best regards, Yao {quote} |
| Description |
Use gene mapping table to add gene descriptions to new annotations bed-detail file for SL5.0 genome assembly release and annotations.
Specifically: * Get the BED-detail gene model file from IGBQuickload repository: http://lorainelab-quickload.scidas.org/quickload/S_lycopersicum_Jun_2022/S_lycopersicum_Jun_2022.bed.gz The 13th column of this file contains a gene identifier. The 4th column contains a transcript identifier. The final (14th) column contains "NA" for "Not Available." We would like it to instead contain a description of the gene. Since we don't have that, we would like to insert the description of gene counterparts present in the SL4.0 annotations. * Note that the SL4 annotations can be found here: http://lorainelab-quickload.scidas.org/quickload/S_lycopersicum_Sep_2019/S_lycopersicum_Sep_2019.bed.gz To map genes from SL4 onto SL5, you need a mapping file. The people who made SL5.0 gave us that mapping file. Author Yao me this: {quote} Dear Ann, Yes, we do have tables for the conversion between different versions. They are now avaiable on our website (http://solomics.agis.org.cn/tomato/ftp/ID_convert/). Thanks so much for the intergration! I would be happy to forward it to my colleagues when it is avaiable. Best regards, Yao {quote} |
Use gene mapping table to add gene descriptions to new annotations bed-detail file for SL5.0 genome assembly release and annotations.
Specifically: * Get the BED-detail gene model file from IGBQuickload repository: http://lorainelab-quickload.scidas.org/quickload/S_lycopersicum_Jun_2022/S_lycopersicum_Jun_2022.bed.gz The 13th column of this file contains a gene identifier. The 4th column contains a transcript identifier. The final (14th) column contains "NA" for "Not Available." We would like it to instead contain a description of the gene. Since we don't have that, we would like to insert the description of gene counterparts present in the SL4.0 annotations. * Note that the SL4 annotations can be found here: http://lorainelab-quickload.scidas.org/quickload/S_lycopersicum_Sep_2019/S_lycopersicum_Sep_2019.bed.gz To map genes from SL4 onto SL5, you need a mapping file. The people who made SL5.0 gave us that mapping file back in July 2022: {quote} Dear Ann, Yes, we do have tables for the conversion between different versions. They are now avaiable on our website (http://solomics.agis.org.cn/tomato/ftp/ID_convert/). Thanks so much for the intergration! I would be happy to forward it to my colleagues when it is avaiable. Best regards, Yao {quote} Mapping files needed are also available in: /nobackup/tomato_genome/alt_splicing/mappingfiles |
| 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 |
| Assignee | Molly Davis [ molly ] |
| Status | To-Do [ 10305 ] | In Progress [ 3 ] |
| Description |
Use gene mapping table to add gene descriptions to new annotations bed-detail file for SL5.0 genome assembly release and annotations.
Specifically: * Get the BED-detail gene model file from IGBQuickload repository: http://lorainelab-quickload.scidas.org/quickload/S_lycopersicum_Jun_2022/S_lycopersicum_Jun_2022.bed.gz The 13th column of this file contains a gene identifier. The 4th column contains a transcript identifier. The final (14th) column contains "NA" for "Not Available." We would like it to instead contain a description of the gene. Since we don't have that, we would like to insert the description of gene counterparts present in the SL4.0 annotations. * Note that the SL4 annotations can be found here: http://lorainelab-quickload.scidas.org/quickload/S_lycopersicum_Sep_2019/S_lycopersicum_Sep_2019.bed.gz To map genes from SL4 onto SL5, you need a mapping file. The people who made SL5.0 gave us that mapping file back in July 2022: {quote} Dear Ann, Yes, we do have tables for the conversion between different versions. They are now avaiable on our website (http://solomics.agis.org.cn/tomato/ftp/ID_convert/). Thanks so much for the intergration! I would be happy to forward it to my colleagues when it is avaiable. Best regards, Yao {quote} Mapping files needed are also available in: /nobackup/tomato_genome/alt_splicing/mappingfiles |
Git repository for this sub-project: https://bitbucket.org/hotpollen/splicing-analysis/src/master/
Use gene mapping table to add gene descriptions to new annotations bed-detail file for SL5.0 genome assembly release and annotations. Specifically: * Get the BED-detail gene model file from IGBQuickload repository: http://lorainelab-quickload.scidas.org/quickload/S_lycopersicum_Jun_2022/S_lycopersicum_Jun_2022.bed.gz The 13th column of this file contains a gene identifier. The 4th column contains a transcript identifier. The final (14th) column contains "NA" for "Not Available." We would like it to instead contain a description of the gene. Since we don't have that, we would like to insert the description of gene counterparts present in the SL4.0 annotations. * Note that the SL4 annotations can be found here: http://lorainelab-quickload.scidas.org/quickload/S_lycopersicum_Sep_2019/S_lycopersicum_Sep_2019.bed.gz To map genes from SL4 onto SL5, you need a mapping file. The people who made SL5.0 gave us that mapping file back in July 2022: {quote} Dear Ann, Yes, we do have tables for the conversion between different versions. They are now avaiable on our website (http://solomics.agis.org.cn/tomato/ftp/ID_convert/). Thanks so much for the intergration! I would be happy to forward it to my colleagues when it is avaiable. Best regards, Yao {quote} Mapping files needed are also available in: /nobackup/tomato_genome/alt_splicing/mappingfiles |
| 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 1 2022 Aug 15, Fall 2 2022 Sep 5 [ 151, 152, 153, 154 ] |
| Rank | Ranked higher |
| 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 ] |
| Sprint | Summer 5 2022 July 18, Summer 6 2022 Aug 1, Fall 1 2022 Aug 15, Fall 2 2022 Sep 5 [ 151, 152, 153, 154 ] | Summer 5 2022 July 18, Summer 6 2022 Aug 1, Fall 1 2022 Aug 15, Fall 2 2022 Sep 5, Fall 3 2022 Sep 26 [ 151, 152, 153, 154, 155 ] |
| Rank | Ranked higher |
| 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 ] |
| Assignee | Molly Davis [ molly ] |
| Sprint | Summer 5 2022 July 18, Summer 6 2022 Aug 1, Fall 1 2022 Aug 15, Fall 2 2022 Sep 5, Fall 3 2022 Sep 26 [ 151, 152, 153, 154, 155 ] | Summer 5 2022 July 18, Summer 6 2022 Aug 1, Fall 1 2022 Aug 15, Fall 2 2022 Sep 5, Fall 3 2022 Sep 26, Fall 4 2022 Oct 10 [ 151, 152, 153, 154, 155, 156 ] |
| Rank | Ranked higher |
| Status | Merged Needs Testing [ 10002 ] | Post-merge Testing In Progress [ 10003 ] |
| Assignee | Ann Loraine [ aloraine ] |
| Status | Post-merge Testing In Progress [ 10003 ] | To-Do [ 10305 ] |
| Assignee | Ann Loraine [ aloraine ] | Molly Davis [ molly ] |
| Sprint | Summer 5 2022 July 18, Summer 6 2022 Aug 1, Fall 1 2022 Aug 15, Fall 2 2022 Sep 5, Fall 3 2022 Sep 26, Fall 4 2022 Oct 10 [ 151, 152, 153, 154, 155, 156 ] | Summer 5 2022 July 18, Summer 6 2022 Aug 1, Fall 1 2022 Aug 15, Fall 2 2022 Sep 5, Fall 3 2022 Sep 26, Fall 4 2022 Oct 10, Fall 5 2022 Oct 24 [ 151, 152, 153, 154, 155, 156, 157 ] |
| Rank | Ranked higher |
| Sprint | Summer 5 2022 July 18, Summer 6 2022 Aug 1, Fall 1 2022 Aug 15, Fall 2 2022 Sep 5, Fall 3 2022 Sep 26, Fall 4 2022 Oct 10, Fall 5 2022 Oct 24 [ 151, 152, 153, 154, 155, 156, 157 ] | Summer 5 2022 July 18, Summer 6 2022 Aug 1, Fall 1 2022 Aug 15, Fall 2 2022 Sep 5, Fall 3 2022 Sep 26, Fall 4 2022 Oct 10, Fall 5 2022 Oct 24, Fall 6 2022 Nov 7 [ 151, 152, 153, 154, 155, 156, 157, 158 ] |
| Rank | Ranked higher |
| 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 ] |
| Status | Pull Request Submitted [ 10101 ] | Reviewing Pull Request [ 10303 ] |
| Assignee | Molly Davis [ molly ] |
| Status | Reviewing Pull Request [ 10303 ] | Merged Needs Testing [ 10002 ] |
| Status | Merged Needs Testing [ 10002 ] | Post-merge Testing In Progress [ 10003 ] |
| Assignee | Ann Loraine [ aloraine ] |
| Status | Post-merge Testing In Progress [ 10003 ] | To-Do [ 10305 ] |
| Assignee | Ann Loraine [ aloraine ] | 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 ] |
| 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 ] |