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  1. IGB
  2. IGBF-3135

Add new tomato genome and annotations to IGB Quickload repository

        Details

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

          Description

          https://www.nature.com/articles/s41586-022-04808-9

          Called SL5.0, it includes gene model annotations that document / predict alternative splicing forms.

          For this task, obtain the sequence and annotations and add them to IGB Quickload as a new version of the tomato genome.

          Data:

            Attachments

            1. ITAG5.0-1.png
              ITAG5.0-1.png
              140 kB
            2. ITAG5.0-2.png
              ITAG5.0-2.png
              36 kB
            3. ITAG5.0-4.png
              ITAG5.0-4.png
              116 kB
            4. ITAG5.0-5.png
              ITAG5.0-5.png
              66 kB
            5. ProtAnnot.paxml
              39 kB

              Issue Links

              blocks

              Task - A task that needs to be done. IGBF-3145 Transfer SL4.0 gene descriptions to SL5.0 annotations

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

              Task - A task that needs to be done. IGBF-3143 Run RNA-Seq data processing pipeline on positive splicing control and experimental samples

              • Major - Major loss of function.
              • Closed

              Task - A task that needs to be done. IGBF-3047 Investigate: New splice variant annotations for tomato

              • Major - Major loss of function.
              • Closed

                Activity

                Ascending order - Click to sort in descending order
                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 relates to IGBF-3047 [ IGBF-3047 ]
                ann.loraine Ann Loraine made changes -
                Description https://www.nature.com/articles/s41586-022-04808-9

                Called SL5.0, it includes gene model annotations that document / predict alternative splicing forms.

                For this task, obtain the sequence and annotations and add them to IGB Quickload as a new version of the tomato genome.

                Data:

                * https://solgenomics.net/ftp/genomes/TGG/
                * gene models: https://solgenomics.net/ftp/genomes/TGG/gff/SL5.0.gff3.gz
                * https://solgenomics.net/ftp/genomes/TGG/genome/SL5.0.fasta.gz
                ann.loraine Ann Loraine made changes -
                Description https://www.nature.com/articles/s41586-022-04808-9

                Called SL5.0, it includes gene model annotations that document / predict alternative splicing forms.

                For this task, obtain the sequence and annotations and add them to IGB Quickload as a new version of the tomato genome.

                Data:

                * https://solgenomics.net/ftp/genomes/TGG/
                * gene models: https://solgenomics.net/ftp/genomes/TGG/gff/SL5.0.gff3.gz
                * https://solgenomics.net/ftp/genomes/TGG/genome/SL5.0.fasta.gz                 		https://www.nature.com/articles/s41586-022-04808-9

                Called SL5.0, it includes gene model annotations that document / predict alternative splicing forms.

                For this task, obtain the sequence and annotations and add them to IGB Quickload as a new version of the tomato genome.

                Data:

                * data directory: https://solgenomics.net/ftp/genomes/TGG/
                * gene models: https://solgenomics.net/ftp/genomes/TGG/gff/SL5.0.gff3.gz
                * genome assembly sequence: https://solgenomics.net/ftp/genomes/TGG/genome/SL5.0.fasta.gz
                ann.loraine Ann Loraine made changes -
                Assignee Ann Loraine [ aloraine ]
                ann.loraine Ann Loraine made changes -
                Status To-Do [ 10305 ] In Progress [ 3 ]
                ann.loraine Ann Loraine made changes -
                Attachment ITAG5.0-1.png [ 17243 ]
                ann.loraine Ann Loraine made changes -
                Attachment ITAG5.0-2.png [ 17244 ]
                ann.loraine Ann Loraine made changes -
                Attachment ITAG5.0-3.png [ 17245 ]
                Attachment ITAG5.0-4.png [ 17246 ]
                Attachment ITAG5.0-5.png [ 17247 ]
                ann.loraine Ann Loraine made changes -
                Attachment ITAG5.0-3.png [ 17245 ]
                ann.loraine Ann Loraine made changes -
                Attachment ProtAnnot.paxml [ 17248 ]
                ann.loraine Ann Loraine made changes -
                Status In Progress [ 3 ] Needs 1st Level Review [ 10005 ]
                ann.loraine Ann Loraine made changes -
                Assignee Ann Loraine [ aloraine ]
                ann.loraine Ann Loraine made changes -
                Story Points 2 0.5
                ann.loraine Ann Loraine made changes -
                Story Points 0.5 1
                nfreese Nowlan Freese made changes -
                Assignee Nowlan Freese [ nfreese ]
                nfreese Nowlan Freese made changes -
                Status Needs 1st Level Review [ 10005 ] First Level Review in Progress [ 10301 ]
                nfreese Nowlan Freese made changes -
                Status First Level Review in Progress [ 10301 ] Needs 1st Level Review [ 10005 ]
                nfreese Nowlan Freese made changes -
                Status Needs 1st Level Review [ 10005 ] First Level Review in Progress [ 10301 ]
                nfreese Nowlan Freese made changes -
                Assignee Nowlan Freese [ nfreese ] Ann Loraine [ aloraine ]
                nfreese Nowlan Freese made changes -
                Status First Level Review in Progress [ 10301 ] Ready for Pull Request [ 10304 ]
                nfreese Nowlan Freese made changes -
                Status Ready for Pull Request [ 10304 ] Pull Request Submitted [ 10101 ]
                nfreese Nowlan Freese made changes -
                Status Pull Request Submitted [ 10101 ] Reviewing Pull Request [ 10303 ]
                nfreese Nowlan Freese made changes -
                Status Reviewing Pull Request [ 10303 ] Merged Needs Testing [ 10002 ]
                nfreese Nowlan Freese made changes -
                Status Merged Needs Testing [ 10002 ] Post-merge Testing In Progress [ 10003 ]
                nfreese Nowlan Freese made changes -
                Resolution Done [ 10000 ]
                Status Post-merge Testing In Progress [ 10003 ] Closed [ 6 ]
                ann.loraine Ann Loraine made changes -
                Link This issue relates to IGBF-3143 [ IGBF-3143 ]
                ann.loraine Ann Loraine made changes -
                Link This issue blocks IGBF-3145 [ IGBF-3145 ]

                  People

                  • Assignee:
                    ann.loraine Ann Loraine
                    Reporter:
                    ann.loraine Ann Loraine
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                    Dates

                    • Created:
                      Updated:
                      Resolved: