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  1. IGB
  2. IGBF-4224

Pull all the chromosome locations for APX for IGB viewing

        Details

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

          GOAL: To identify all APX gene locations in SL4 genome using the GFF file.

          Search through the GFF file (SL4 version, ITAG 4.0) for each instance of ascorbate peroxidase.

          We are looking for lines that are "genes" and not exons, etc. Need to genome coordinates
          Chromosome #, start position and stop position.

          Make a summary of all of these and save to a file.

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              abecerri Alex Becerril Cruz (Inactive) added a comment -

              https://docs.google.com/presentation/d/1T-HLpRvbvIpFjkpkfcUNCojsKQ3uHOaZzZ0SWkBI-uc/edit?usp=sharing

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              abecerri Alex Becerril Cruz (Inactive) added a comment - https://docs.google.com/presentation/d/1T-HLpRvbvIpFjkpkfcUNCojsKQ3uHOaZzZ0SWkBI-uc/edit?usp=sharing
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              bbendick Brandon Bendickson added a comment -

              Scale the Y-axis to all be the same.

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              bbendick Brandon Bendickson added a comment - Scale the Y-axis to all be the same.
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              abecerri Alex Becerril Cruz (Inactive) added a comment -

              Here are the chromosomes that I found:
              https://docs.google.com/spreadsheets/d/1Fes2tuad0hVGBUKESWXlRHsfsb1ZZ1WAnvnv7xycCiM/edit?usp=sharing

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              abecerri Alex Becerril Cruz (Inactive) added a comment - Here are the chromosomes that I found: https://docs.google.com/spreadsheets/d/1Fes2tuad0hVGBUKESWXlRHsfsb1ZZ1WAnvnv7xycCiM/edit?usp=sharing
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              robofjoy Robert Reid added a comment -

              The GFF file is needed to get the coords.

              https://drive.google.com/file/d/17VrqLTWJiUe644fHVrjWy2-BWZUj7epv/view?usp=drive_link

              Find each "gene" that is ascorbate peroxidase. Get coords, the chromosme and start and stop positions.

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              robofjoy Robert Reid added a comment - The GFF file is needed to get the coords. https://drive.google.com/file/d/17VrqLTWJiUe644fHVrjWy2-BWZUj7epv/view?usp=drive_link Find each "gene" that is ascorbate peroxidase. Get coords, the chromosme and start and stop positions.

                People

                • Assignee:
                  abecerri Alex Becerril Cruz (Inactive)
                  Reporter:
                  robofjoy Robert Reid
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                  Dates

                  • Created:
                    Updated:
                    Resolved: