UAB Galaxy Workshop Tutorial: Difference between revisions

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= UAB Galaxy Tutorial =
= Overview =


== 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.
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 ==
== Getting Started 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.
RCD 2011 Welcome to Galaxy Tutorial [[media:RCD 2011 Welcome to Galaxy tutorial.pdf|PDF]] or [ftp://ftp.genome.uab.edu/ICS/Galaxy_RNAseq_tutorial/RCD%202011%20Welcome%20to%20Galaxy%20tutorial.pptx PPTX (animations)]


== Galaxy Data Import ==


=== Getting data into Galaxy ===
There are a number of options to upload data:
 
* Uploading through the browser (http) '''!!Max 2G file size!!'''
There are a number of options:
* Copying files to cheaha and linking them in (sftp and scp)
* Uploading through the browser (http)
* 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].
 
=== Linking to a pre-existing data library ===
 
 
=== Assessing the quality of the data ===
 
 
=== Performing cleanup ===
 
 
=== Short read alignment to reference genome using BWA ===


= [[Galaxy DNA-Seq 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.
Go to [[Galaxy DNA-Seq Tutorial]] wiki page.


=== Looking at differences with SNPEff ===
Presentation [[media:RCD2011_DNA-Seq_Workshop_Talk.pdf‎|PDF]] or original [ftp://ftp.genome.uab.edu/ICS/Galaxy_RNAseq_tutorial/RCD2011%20DNA-Seq%20Workshop%20Talk.pptx PPTX].


= [[UAB_Galaxy_RNA_Seq_Step_by_Step_Tutorial|Galaxy RNA-Seq Tutorial]] =


=== De novo assembly (time permitting) ===
For the purpose of realism, simplicity and speed, this tutorial uses a small portion of a real mouse dataset that has kindly been provided by Dr. Kim Keeling. Our object is to determine gene expression differences between the control cells and the drugged cells.


Go to [[UAB_Galaxy_RNA_Seq_Step_by_Step_Tutorial|Galaxy RNA-Seq Tutorial]].


=== Viewing results in IGV ===
= [[Galaxy Workflow Tutorial]] =
This will cover use and creation of galaxy workflows.


== UAB Galaxy RNA-Seq Step-by-Step Tutorial ==
= [[Galaxy Advanced Topics]] =
This will cover topics such as doing galaxy development with git, customizing galaxy and running a personal instance of galaxy on cheaha.

Latest revision as of 08:15, 16 September 2011

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.

Getting Started Tutorial

RCD 2011 Welcome to Galaxy Tutorial PDF or PPTX (animations)

Galaxy Data Import

There are a number of options to upload data:

  • Uploading through the browser (http) !!Max 2G file size!!
  • Copying files to cheaha and linking them in (sftp and scp)
  • Linking to an existing data library

An explanation of the tradeoffs can be found in this mini tutorial on uploading files.

Galaxy DNA-Seq 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.

Go to Galaxy DNA-Seq Tutorial wiki page.

Presentation PDF or original PPTX.

Galaxy RNA-Seq Tutorial

For the purpose of realism, simplicity and speed, this tutorial uses a small portion of a real mouse dataset that has kindly been provided by Dr. Kim Keeling. Our object is to determine gene expression differences between the control cells and the drugged cells.

Go to Galaxy RNA-Seq Tutorial.

Galaxy Workflow Tutorial

This will cover use and creation of galaxy workflows.

Galaxy Advanced Topics

This will cover topics such as doing galaxy development with git, customizing galaxy and running a personal instance of galaxy on cheaha.

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