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  1. IGB
  2. IGBF-4044

Get familiar with InterproScan on the HPC

        Details

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

          GOAL:
          To get familiar with Interproscan so that we can annotate the remaining genes that lack an SL5 or NR DB annotation.

          Need to get the tool ready for using. It has been a few years since it has been used and the ENV has changed. Hopefully the tool still works as is.

          We need to identify what sequences we wish to run through.

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              robofjoy Robert Reid added a comment -

              1st steps:

              Make a sequences file 1000 and run it through the web based version.

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              robofjoy Robert Reid added a comment - 1st steps: Make a sequences file 1000 and run it through the web based version.
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              bbendick Brandon Bendickson added a comment -

              Successfully ran on 2 of the tomato groups on the cluster. Going to relaunch and get outputs for the other two that did not complete.

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              bbendick Brandon Bendickson added a comment - Successfully ran on 2 of the tomato groups on the cluster. Going to relaunch and get outputs for the other two that did not complete.
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              bbendick Brandon Bendickson added a comment -

              Results will be found in: /projects/tomato_genome/fnb/dataprocessing/brandon_work/InterProScan/newest_version/interproscan-5.72-103.0/outputdir

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              bbendick Brandon Bendickson added a comment - Results will be found in: /projects/tomato_genome/fnb/dataprocessing/brandon_work/InterProScan/newest_version/interproscan-5.72-103.0/outputdir
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              bbendick Brandon Bendickson added a comment -

              Interpro analysis for all 4 varieties has completed and results are found in: /projects/tomato_genome/fnb/dataprocessing/brandon_work/InterProScan/newest_version/interproscan-5.72-103.0/outputdir

              Assigning to Dr. Reid to take a look at results.

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              bbendick Brandon Bendickson added a comment - Interpro analysis for all 4 varieties has completed and results are found in: /projects/tomato_genome/fnb/dataprocessing/brandon_work/InterProScan/newest_version/interproscan-5.72-103.0/outputdir Assigning to Dr. Reid to take a look at results.
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              robofjoy Robert Reid added a comment -

              This as first glance looks like the data we'd expect.

              Next phase!!

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              robofjoy Robert Reid added a comment - This as first glance looks like the data we'd expect. Next phase!!

                People

                • Assignee:
                  robofjoy Robert Reid
                  Reporter:
                  robofjoy Robert Reid
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                  Dates

                  • Created:
                    Updated:
                    Resolved: