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Galaxy DNA-Seq Tutorial

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Revision as of 15:29, 13 September 2011 by Ozborn@uab.edu (Talk | contribs)

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Contents

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"
  • Click on "Analyze Data" from the upper main menu. It should bring up the main page and your history pane should now look like the image below.

HistoryPane.jpg

  • Notice that with just 3 viruses are already over 4 GB of data.
  • Click on the pencil to icon in one of the virus images to pull up the attributes, your screen should look a bit like this:

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