UAB Galaxy Workshop Tutorial - Revision history

Curtish@uab.edu: /* Getting Started Tutorial */

2011-09-16T08:15:48Z

Getting Started Tutorial

← Older revision		Revision as of 08:15, 16 September 2011
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	== Getting Started Tutorial ==		== Getting Started Tutorial ==

	RCD 2011 Welcome to Galaxy Tutorial [[~~File~~: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)]		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 ==		== Galaxy Data Import ==

Curtish@uab.edu: /* Galaxy DNA-Seq Tutorial */

2011-09-16T08:15:11Z

Galaxy DNA-Seq Tutorial

← Older revision		Revision as of 08:15, 16 September 2011
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	Go to [[Galaxy DNA-Seq Tutorial]] wiki page.		Go to [[Galaxy DNA-Seq Tutorial]] wiki page.

	Presentation [[~~File~~: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].		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]] =		= [[UAB_Galaxy_RNA_Seq_Step_by_Step_Tutorial\|Galaxy RNA-Seq Tutorial]] =

Curtish@uab.edu: /* Getting Started Tutorial */

2011-09-16T08:11:26Z

Getting Started Tutorial

← Older revision		Revision as of 08:11, 16 September 2011
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	== Getting Started Tutorial ==		== Getting Started Tutorial ==

	RCD 2011 Welcome to Galaxy Tutorial [[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)]		RCD 2011 Welcome to Galaxy Tutorial [[File: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 ==		== Galaxy Data Import ==

Curtish@uab.edu: /* Galaxy DNA-Seq Tutorial */

2011-09-16T08:11:08Z

Galaxy DNA-Seq Tutorial

← Older revision		Revision as of 08:11, 16 September 2011
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	Go to [[Galaxy DNA-Seq Tutorial]] wiki page.		Go to [[Galaxy DNA-Seq Tutorial]] wiki page.

	Presentation [[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].		Presentation [[File: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]] =		= [[UAB_Galaxy_RNA_Seq_Step_by_Step_Tutorial\|Galaxy RNA-Seq Tutorial]] =

Curtish@uab.edu: /* Galaxy DNA-Seq Tutorial */

2011-09-16T08:10:34Z

Galaxy DNA-Seq Tutorial

← Older revision		Revision as of 08:10, 16 September 2011
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	Go to [[Galaxy DNA-Seq Tutorial]] wiki page.		Go to [[Galaxy DNA-Seq Tutorial]] wiki page.
	Presentation [[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].
			Presentation [[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]] =		= [[UAB_Galaxy_RNA_Seq_Step_by_Step_Tutorial\|Galaxy RNA-Seq Tutorial]] =

Curtish@uab.edu: /* Galaxy DNA-Seq Tutorial */

2011-09-16T08:10:05Z

Galaxy DNA-Seq Tutorial

← Older revision		Revision as of 08:10, 16 September 2011
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	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.		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]].		Go to [[Galaxy DNA-Seq Tutorial]] wiki page.
			Presentation [[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]] =		= [[UAB_Galaxy_RNA_Seq_Step_by_Step_Tutorial\|Galaxy RNA-Seq Tutorial]] =

Curtish@uab.edu: /* Galaxy DNA-Seq Tutorial */

2011-09-16T06:31:58Z

Galaxy DNA-Seq Tutorial

← Older revision		Revision as of 06:31, 16 September 2011
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	= [[Galaxy DNA-Seq Tutorial]] =		= [[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.		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]].

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

Curtish@uab.edu: /* Galaxy RNA-Seq Tutorial */

2011-09-16T06:31:40Z

Galaxy RNA-Seq Tutorial

← Older revision		Revision as of 06:31, 16 September 2011
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	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.		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]].

	= [[Galaxy Workflow Tutorial]] =		= [[Galaxy Workflow Tutorial]] =

Curtish@uab.edu: /* Galaxy RNA-Seq Tutorial */

2011-09-16T06:30:10Z

Galaxy RNA-Seq Tutorial

← Older revision		Revision as of 06:30, 16 September 2011
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	= [[UAB_Galaxy_RNA_Seq_Step_by_Step_Tutorial\|Galaxy RNA-Seq Tutorial]] =		= [[UAB_Galaxy_RNA_Seq_Step_by_Step_Tutorial\|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.

	= [[Galaxy Workflow Tutorial]] =		= [[Galaxy Workflow Tutorial]] =

Curtish@uab.edu: /* UAB Galaxy Tutorial */

2011-09-16T06:26:16Z

UAB Galaxy Tutorial

← Older revision		Revision as of 06:26, 16 September 2011
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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.

	=== Getting Started Tutorial ===		== Getting Started Tutorial ==

	RCD 2011 Welcome to Galaxy Tutorial [[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)]		RCD 2011 Welcome to Galaxy Tutorial [[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 ===		== Galaxy Data Import ==

	There are a number of options to upload data:		There are a number of options to upload data:
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	An explanation of the tradeoffs can be found in this mini tutorial on [http://projects.uabgrid.uab.edu/galaxy/wiki/UploadingFiles uploading files].		An explanation of the tradeoffs can be found in this mini tutorial on [http://projects.uabgrid.uab.edu/galaxy/wiki/UploadingFiles uploading files].

	== [[Galaxy DNA-Seq Tutorial]] ==		= [[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.		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.

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

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

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