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  1. IGB
  2. IGBF-1522

Write program to convert EnsGene table bed12 to bed14

        Details

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

          Write a python program that accepts data from Ensembl BioMart and from UCSC Table Browser EnsGene table and produces bed14 format file.

          • Field 4 contains Ensembl transcript id (e.g., ENSCSAT00000001292.1)
          • Field 13 contains Ensembl gene id for the transcript (e.g., ENSCSAG00000003267.1) from BioMart
          • Field 14 contains descriptive information from BioMart

          The key work of this script is to cross-reference gene ids and functional descriptions obtained from BioMart with transcript ids obtained from UCSC Genome Browser.

          We developed this so that we could include vervet (African green monkey) gene annotations in IGB Quickload, a user request.

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              relates to

              Task - A task that needs to be done. IGBF-1401 Add Chlorocebus sabaeus ("green monkey") to IGB quickload

              • Major - Major loss of function.
              • Closed

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                  People

                  • Assignee:
                    Jill Jill Jenkins (Inactive)
                    Reporter:
                    ann.loraine Ann Loraine
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                    • Created:
                      Updated:
                      Resolved: