Uploaded image for project: 'IGB'
  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
        • Labels:
          None

          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.

            Attachments

              Activity

              Ascending order - Click to sort in descending order
              Hide
              Permalink
              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.

              Show
              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.
              Hide
              Permalink
              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

              Show
              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
              Hide
              Permalink
              bbendick Brandon Bendickson added a comment -

              Scale the Y-axis to all be the same.

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

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

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

                People

                • Assignee:
                  abecerri Alex Becerril Cruz (Inactive)
                  Reporter:
                  robofjoy Robert Reid
                • Votes:
                  0 Vote for this issue
                  Watchers:
                  3 Start watching this issue

                  Dates

                  • Created:
                    Updated:
                    Resolved: