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  1. IGB
  2. IGBF-3145

Transfer SL4.0 gene descriptions to SL5.0 annotations

        Details

        • Type: Task
        • Status: Closed (View Workflow)
        • Priority: Major
        • Resolution: Done
        • Affects Version/s: None
        • Fix Version/s: None
        • Labels:
          None
        • Story Points:
          0.25
        • Epic Link:
        • 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:

          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.

          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

              is blocked by

              Task - A task that needs to be done. IGBF-3135 Add new tomato genome and annotations to IGB Quickload repository

              • Major - Major loss of function.
              • Closed
              relates to

              Task - A task that needs to be done. IGBF-3229 Complete gene description transfer

              • Blocker - Blocks development and/or testing work, production could not run.
              • Closed

                Activity

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                ann.loraine Ann Loraine created issue -
                ann.loraine Ann Loraine made changes -
                Field Original Value New Value
                Epic Link IGBF-2993 [ 21429 ]
                ann.loraine Ann Loraine made changes -
                Link This issue is blocked by IGBF-3135 [ IGBF-3135 ]
                ann.loraine Ann Loraine made changes -
                Sprint Summer 5 2022 July 18 [ 151 ] Summer 5 2022 July 18, Summer 6 2022 Aug 1 [ 151, 152 ]
                ann.loraine Ann Loraine made changes -
                Rank Ranked higher
                ann.loraine Ann Loraine made changes -
                Rank Ranked higher
                ann.loraine Ann Loraine made changes -
                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
                ann.loraine Ann Loraine made changes -
                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.
                ann.loraine Ann Loraine made changes -
                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}

                ann.loraine Ann Loraine made changes -
                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

                ann.loraine Ann Loraine made changes -
                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 ]
                ann.loraine Ann Loraine made changes -
                Rank Ranked higher
                Mdavis4290 Molly Davis made changes -
                Assignee Molly Davis [ molly ]
                ann.loraine Ann Loraine made changes -
                Status To-Do [ 10305 ] In Progress [ 3 ]
                ann.loraine Ann Loraine made changes -
                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

                ann.loraine Ann Loraine made changes -
                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 ]
                ann.loraine Ann Loraine made changes -
                Rank Ranked higher
                ann.loraine Ann Loraine made changes -
                Status In Progress [ 3 ] Needs 1st Level Review [ 10005 ]
                ann.loraine Ann Loraine made changes -
                Status Needs 1st Level Review [ 10005 ] First Level Review in Progress [ 10301 ]
                ann.loraine Ann Loraine made changes -
                Status First Level Review in Progress [ 10301 ] Ready for Pull Request [ 10304 ]
                nfreese Nowlan Freese made changes -
                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 ]
                nfreese Nowlan Freese made changes -
                Rank Ranked higher
                ann.loraine Ann Loraine made changes -
                Status Ready for Pull Request [ 10304 ] Pull Request Submitted [ 10101 ]
                ann.loraine Ann Loraine made changes -
                Status Pull Request Submitted [ 10101 ] Reviewing Pull Request [ 10303 ]
                ann.loraine Ann Loraine made changes -
                Status Reviewing Pull Request [ 10303 ] Merged Needs Testing [ 10002 ]
                ann.loraine Ann Loraine made changes -
                Assignee Molly Davis [ molly ]
                ann.loraine Ann Loraine made changes -
                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 ]
                ann.loraine Ann Loraine made changes -
                Rank Ranked higher
                ann.loraine Ann Loraine made changes -
                Status Merged Needs Testing [ 10002 ] Post-merge Testing In Progress [ 10003 ]
                ann.loraine Ann Loraine made changes -
                Assignee Ann Loraine [ aloraine ]
                ann.loraine Ann Loraine made changes -
                Status Post-merge Testing In Progress [ 10003 ] To-Do [ 10305 ]
                ann.loraine Ann Loraine made changes -
                Assignee Ann Loraine [ aloraine ] Molly Davis [ molly ]
                nfreese Nowlan Freese made changes -
                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 ]
                nfreese Nowlan Freese made changes -
                Rank Ranked higher
                ann.loraine Ann Loraine made changes -
                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 ]
                ann.loraine Ann Loraine made changes -
                Rank Ranked higher
                ann.loraine Ann Loraine made changes -
                Status To-Do [ 10305 ] In Progress [ 3 ]
                ann.loraine Ann Loraine made changes -
                Status In Progress [ 3 ] Needs 1st Level Review [ 10005 ]
                ann.loraine Ann Loraine made changes -
                Status Needs 1st Level Review [ 10005 ] First Level Review in Progress [ 10301 ]
                ann.loraine Ann Loraine made changes -
                Status First Level Review in Progress [ 10301 ] Ready for Pull Request [ 10304 ]
                ann.loraine Ann Loraine made changes -
                Status Ready for Pull Request [ 10304 ] Pull Request Submitted [ 10101 ]
                ann.loraine Ann Loraine made changes -
                Status Pull Request Submitted [ 10101 ] Reviewing Pull Request [ 10303 ]
                ann.loraine Ann Loraine made changes -
                Assignee Molly Davis [ molly ]
                ann.loraine Ann Loraine made changes -
                Status Reviewing Pull Request [ 10303 ] Merged Needs Testing [ 10002 ]
                ann.loraine Ann Loraine made changes -
                Status Merged Needs Testing [ 10002 ] Post-merge Testing In Progress [ 10003 ]
                ann.loraine Ann Loraine made changes -
                Assignee Ann Loraine [ aloraine ]
                ann.loraine Ann Loraine made changes -
                Status Post-merge Testing In Progress [ 10003 ] To-Do [ 10305 ]
                ann.loraine Ann Loraine made changes -
                Assignee Ann Loraine [ aloraine ] Molly Davis [ molly ]
                ann.loraine Ann Loraine made changes -
                Link This issue relates to IGBF-3229 [ IGBF-3229 ]
                ann.loraine Ann Loraine made changes -
                Status To-Do [ 10305 ] In Progress [ 3 ]
                ann.loraine Ann Loraine made changes -
                Status In Progress [ 3 ] Needs 1st Level Review [ 10005 ]
                ann.loraine Ann Loraine made changes -
                Status Needs 1st Level Review [ 10005 ] First Level Review in Progress [ 10301 ]
                ann.loraine Ann Loraine made changes -
                Status First Level Review in Progress [ 10301 ] Ready for Pull Request [ 10304 ]
                ann.loraine Ann Loraine made changes -
                Status Ready for Pull Request [ 10304 ] Pull Request Submitted [ 10101 ]
                ann.loraine Ann Loraine made changes -
                Status Pull Request Submitted [ 10101 ] Reviewing Pull Request [ 10303 ]
                ann.loraine Ann Loraine made changes -
                Status Reviewing Pull Request [ 10303 ] Merged Needs Testing [ 10002 ]
                ann.loraine Ann Loraine made changes -
                Status Merged Needs Testing [ 10002 ] Post-merge Testing In Progress [ 10003 ]
                ann.loraine Ann Loraine made changes -
                Resolution Done [ 10000 ]
                Status Post-merge Testing In Progress [ 10003 ] Closed [ 6 ]

                  People

                  • Assignee:
                    Mdavis4290 Molly Davis
                    Reporter:
                    ann.loraine Ann Loraine
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                    Dates

                    • Created:
                      Updated:
                      Resolved: