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  1. IGB
  2. IGBF-3733

Parse Trinity/Blat results to identify contigs that can be annotated

        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: Devise a strategy to annotate the Trinity results generated in IGBF-3647.

          We have MANY contigs (170K or more per variety).

          Step 1 would be to identify how many contigs align to a corresponding soly gene (via our blat results).
          Step 2: How many trinity contigs fail to have a match?
          Step 3: How many contigs are promiscuous and have many gene matches?
          Step 4: How many Soly Ids have only 1 Trinity Contig match? (best hit recprical)

          From this we will decide if these associations are suitable to be used as annotations.

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              Task - A task that needs to be done. IGBF-3732 Prepare Google slide deck outlining reference free pipeline + results(Kelsey)

              • Minor - Minor loss of function, or other problem where easy workaround is present.
              • Closed

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                  • Assignee:
                    bbendick Brandon Bendickson
                    Reporter:
                    robofjoy Robert Reid
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                      Updated:
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