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  1. IGB
  2. IGBF-4114

Run Transdecoder

        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: Run Transdecoder on de novo contigs.
          Make a new fasta of the longest ORFs at the protein level.
          Summarize these numbers at the NT and AA level.

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              bbendick Brandon Bendickson added a comment -

              successfully ran transdecoder on our unfiltered contigs. Results are found in: /projects/tomato_genome/fnb/dataprocessing/brandon_work/Transdecoder/unfiltered_contigs

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              bbendick Brandon Bendickson added a comment - successfully ran transdecoder on our unfiltered contigs. Results are found in: /projects/tomato_genome/fnb/dataprocessing/brandon_work/Transdecoder/unfiltered_contigs
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              bbendick Brandon Bendickson added a comment -

              Also ran on FCS filtered contigs. Results are found in: /projects/tomato_genome/fnb/dataprocessing/brandon_work/Transdecoder/FCS_filtered_contigs

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              bbendick Brandon Bendickson added a comment - Also ran on FCS filtered contigs. Results are found in: /projects/tomato_genome/fnb/dataprocessing/brandon_work/Transdecoder/FCS_filtered_contigs
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              bbendick Brandon Bendickson added a comment -

              Significantly less putative proteins between filtered/unfiltered runs.

              File: hei_longhit.fna.transdecoder.pep
              Number of sequences: 55047

              File: heinz_filtered.fa.transdecoder.pep
              Number of sequences: 32447

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              bbendick Brandon Bendickson added a comment - Significantly less putative proteins between filtered/unfiltered runs. File: hei_longhit.fna.transdecoder.pep Number of sequences: 55047 File: heinz_filtered.fa.transdecoder.pep Number of sequences: 32447
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              robofjoy Robert Reid added a comment -

              These results look great.

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              robofjoy Robert Reid added a comment - These results look great.

                People

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

                  • Created:
                    Updated:
                    Resolved: