Namespaces

Variants
Actions
Personal tools

UAB Galaxy Workshop Tutorial

From UABgrid Documentation

(Difference between revisions)
Jump to: navigation, search
(Getting data into Galaxy)
(Getting data into Galaxy: Added links to data uploading, still need cleanup.)
Line 11: Line 11:
 
=== Getting data into Galaxy ===
 
=== Getting data into Galaxy ===
  
There are a number of options:
+
There are a number of options to [[UploadLargeData]].
 
* Uploading through the browser (http)
 
* Uploading through the browser (http)
 
* Copying files to cheaha and linking them in (ftp and scp)
 
* Copying files to cheaha and linking them in (ftp and scp)
 
* Linking to an existing data library
 
* Linking to an existing data library
  
An explaination of the tradeoffs can be found [http://projects.uabgrid.uab.edu/galaxy/wiki/UploadingFiles here]. For this tutorial we will be linking in a library that has already been uploaded.
+
An explanation of the tradeoffs can be found in this mini tutorial on [http://projects.uabgrid.uab.edu/galaxy/wiki/UploadingFiles uploading files]. For this tutorial we will be linking in a [http://projects.uabgrid.uab.edu/galaxy/wiki/DataLibraries data library] that has already been uploaded.
  
 
=== Linking to a pre-existing data library ===
 
=== Linking to a pre-existing data library ===

Revision as of 11:59, 13 September 2011

Contents

UAB Galaxy Tutorial

Overview

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 to UploadLargeData.

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

An explanation of the tradeoffs can be found in this mini tutorial on uploading files. For this tutorial we will be linking in a data 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