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Galaxy DNA-Seq Tutorial

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Galaxy DNA-Seq Tutorial

Linking to data

Link in the Mark Pritchard Vaccinia virus data set.

  • Start with a blank history, there should be no numbered items on the right hand side of the pane. Otherwise create a new history.
  • Select "Shared Data" from the top of the screen to bring up the Shared Data screen
  • Select "Mark Pritchard Vaccinia WR" from the alphabetically sorted list
  • Click the top box to select all 6 files
  • Select "import to current history"

Formatting and Grooming Data

Assessing the quality of the data

Performing cleanup

Short read alignment to reference genome using BWA

Looking at differences with SNPEff

De novo assembly (time permitting)

Viewing results in IGV