Namespaces

Variants
Actions
Personal tools

Galaxy DNA-Seq Tutorial

From UABgrid Documentation

Revision as of 13:34, 13 September 2011 by Ozborn@uab.edu (Talk | contribs)

Jump to: navigation, search

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"

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