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  1. IGB
  2. IGBF-3741

Align Trinity Contigs to SL4 & SL5 via BLAT

        Details

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

          Goal is to visualize how the BLAT alignments look.
          To do this we need to align contigs to SL4 and SL5 genome (and not to CDS).

          But before we do this, we want to implement Ann's suggestions for blat parameters. (e.g., max intron size:10K)

          The current blat command being used is this:

          blat /projects/tomato_genome/db/SL5/SL5.cds.fa \
          /dev/null /dev/null -tileSize=11 -makeOoc=$

          {file}

          .11.ooc -repMatch=1024

          Script will point to proper reference genome files.
          And we will incorporate other parameters as Ann suggests.
          which are..........

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