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UAB Galaxy Workshop Tutorial

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UAB Galaxy Tutorial


Time is limited, but this tutorial will account creation and logging in to galaxy and the cheaha cluster. This will be followed by a short but important section of how to get your data into galaxy and then finally tutorials on 2 common tasks: DNA-Seq and RNA-Seq. If there is time there will be an advanced section on workflow creation, Galaxy development and running your own personal galaxy instance.

UAB Galaxy DNA-Seq Step-by-Step Tutorial

For the purpose of realism, simplicity and speed, this tutorial uses a portion of a real virus dataset that has kindly been provided by Dr. Mark Prichard and was one of the first NextGen sequencing projects undertaken by CCTS. Our object is to process the results from 2 viruses, a wild type Vaccinia virus and a derived mutant strain and analyze the differences in Galaxy.

Getting data into Galaxy

There are a number of options:

  • Uploading through the browser (http)
  • Copying files to cheaha and linking them in (ftp and scp)
  • Linking to an existing data library

An explaination of the tradeoffs can be found here. For this tutorial we will be linking in a library that has already been uploaded.

Linking to a pre-existing data library

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

UAB Galaxy RNA-Seq Step-by-Step Tutorial