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  1. IGB
  2. IGBF-4107

Blast de novo contigs against 4 contaminants

        Details

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

          Description

          GOAL:

          To write a script on the cluster based on previous scripts to BLAST
          our de novo contigs against the 4 main contaminants found via the FCS filter tool.

          The 4 contaminants are in:
          /projects/tomato_genome/db/contaminants/

          1. sclerotinia_minor
          2. Sclerotinia_sclerotiorum
          3. Pseudocercospora_ulei
          4. Cladosporium_colombiae

          These were pulled from NCBI as full genomes.

          Need to makeblastDB for each contaminant.

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              robofjoy Robert Reid added a comment -

              Note: This is related to ticket IGBF-4093, the tomato mold story.

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              robofjoy Robert Reid added a comment - Note: This is related to ticket IGBF-4093 , the tomato mold story.
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              bbendick Brandon Bendickson added a comment -

              Storing BLAST information on this sheet: https://docs.google.com/spreadsheets/d/1HeMRLHCuAZsEoXIq4sxLkK8qyuVMRkBzTQBsngx2IdE/edit?usp=sharing

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              bbendick Brandon Bendickson added a comment - Storing BLAST information on this sheet: https://docs.google.com/spreadsheets/d/1HeMRLHCuAZsEoXIq4sxLkK8qyuVMRkBzTQBsngx2IdE/edit?usp=sharing
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              bbendick Brandon Bendickson added a comment - - edited

              -rerun at 1e-25
              -get unique query IDs
              -get number of hits
              -make chart with this info

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              bbendick Brandon Bendickson added a comment - - edited -rerun at 1e-25 -get unique query IDs -get number of hits -make chart with this info

                People

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

                  • Created:
                    Updated:
                    Resolved: