Course: Bioinformatics for Biomedical Research (2014). Session: 2.2- Introduction to Galaxy. A web-based genome analysis platform. Statistics and Bioinformatisc Unit (UEB) & High Technology Unit (UAT) from Vall d'Hebron Research Institute (www.vhir.org), Barcelona.

1. 1
Vall d’Hebron Institut de Recerca (VHIR)
Alex Sánchez
15/05/2014
Institut d’Investigació Sanitària acreditat per l’Instituto de Salud Carlos III (ISCIII)
Introduction to Galaxy
A web-based genome analysis platform
BIOINFORMATICS FOR
BIOMEDICAL RESEARCH

2. 2
• Galaxy overview and Interface
• Getting Data in Galaxy
• Analyzing Data in Galaxy
– Quality Control
– Mapping Data
• History and workflow
• Galaxy Exercises
NGS Analysis Using Galaxy

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What is Galaxy
• Galaxy is an open-source framework for
integrating various computational tools and
databases into a cohesive workspace.
But it can also be seen as
• A web-based service, integrating many popular
tools and resources for comparative genomics.
And also
• A completely self-contained application for
building your own Galaxy style sites.

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http://galaxyproject.org

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Galaxy Conceptual Framework

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Galaxy Interface Sections
contains links to
the downloading,
preparation and
analysis tools.
The center column
is where the
menus and data
will appear
show you the history
of your analysis steps,
allow you view data
and results, and more.
RegisterUser

7. 77
Getting Data
Click Get Data

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Getting Data: Table Browser
Get Table Main

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Getting Data: UCSC Table Browser
Get Output
clade: Mammal
genome: Human
assmbly: [current]
group: Genes and…
track: UCSC Genes
table: knownGene
region: position, chrX
Output format:
BED, and check
Send output to
Galaxy

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Getting Data: Upload File
Upload File
Execute
File Format
Species
Upload or paste file

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Getting Data: Upload File
Specify multiple URLs
into the "URL / Text" box

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• Sequences and Alignment Format
• Galaxy overview and Interface
• Getting Data in Galaxy
• Analyzing Data in Galaxy
– Text Manipulation tools
– Filter and Sort
– Operate on Genomic Intervals
– Quality Control
– Mapping Data
• History and workflow
• Galaxy Exercises
NGS Analysis Using Galaxy

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Text Manipulation Tools

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Filter and Sort

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Operate on Genomic Intervals

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Fasta Manipulation

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Analyzing Data: Next Generation Sequencing

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Analyzing Data: Next Generation Sequencing
FASTQ file manipulation,
like format conversation,
summary statistics,
trimming reads,
filtering reads
by quality score…

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Analyzing Data: Next Generation Sequencing
Input: sanger FASTQ
Output: SAM format

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Analyzing Data: Next Generation Sequencing

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• Sequences and Alignment Format
• Galaxy overview and Interface
• Getting Data in Galaxy
• Analyzing Data in Galaxy
– Quality Control
– Mapping Data
• History and workflow
• Galaxy Exercises
NGS Analysis Using Galaxy

22. 22Copyright OpenHelix. No use or
reproduction without express written
22
History: History Options
List saved histories and
shared histories.
Work on Current History,
create new, clone, share,
create workflow, set
permissions, show deleted
datasets or delete history.
List saved histories

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Workflow
Creates a workflow, allows
user to repeat analysis
using different datasets.

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• Sequences and Alignment Format
• Galaxy overview and Interface
• Getting Data in Galaxy
• Analyzing Data in Galaxy
– Quality Control
– Mapping Data
• History and workflow
• Galaxy Exercises
NGS Analysis Using Galaxy