1
Vall d’Hebron Institut de Recerca (VHIR)
Alex Sánchez
15/05/2014
Institut d’Investigació Sanitària acreditat per l’Insti...
2
• Galaxy overview and Interface
• Getting Data in Galaxy
• Analyzing Data in Galaxy
– Quality Control
– Mapping Data
• H...
3
What is Galaxy
• Galaxy is an open-source framework for
integrating various computational tools and
databases into a coh...
4
http://galaxyproject.org
5
Galaxy Conceptual Framework
66
Galaxy Interface Sections
contains links to
the downloading,
preparation and
analysis tools.
The center column
is where...
77
Getting Data
Click Get Data
88
Getting Data: Table Browser
Get Table Main
99
Getting Data: UCSC Table Browser
Get Output
clade: Mammal
genome: Human
assmbly: [current]
group: Genes and…
track: UCS...
1010
Getting Data: Upload File
Upload File
Execute
File Format
Species
Upload or paste file
11
Getting Data: Upload File
Specify multiple URLs
into the "URL / Text" box
12
• Sequences and Alignment Format
• Galaxy overview and Interface
• Getting Data in Galaxy
• Analyzing Data in Galaxy
– ...
13
Text Manipulation Tools
14
Filter and Sort
15
Operate on Genomic Intervals
16
Fasta Manipulation
1717
Analyzing Data: Next Generation Sequencing
18
Analyzing Data: Next Generation Sequencing
FASTQ file manipulation,
like format conversation,
summary statistics,
trimm...
19
Analyzing Data: Next Generation Sequencing
Input: sanger FASTQ
Output: SAM format
20
Analyzing Data: Next Generation Sequencing
21
• Sequences and Alignment Format
• Galaxy overview and Interface
• Getting Data in Galaxy
• Analyzing Data in Galaxy
– ...
22Copyright OpenHelix. No use or
reproduction without express written
22
History: History Options
List saved histories and...
23
Workflow
Creates a workflow, allows
user to repeat analysis
using different datasets.
24
• Sequences and Alignment Format
• Galaxy overview and Interface
• Getting Data in Galaxy
• Analyzing Data in Galaxy
– ...
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Introduction to Galaxy (UEB-UAT Bioinformatics Course - Session 2.2 - VHIR, Barcelona)

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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.

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Introduction to Galaxy (UEB-UAT Bioinformatics Course - Session 2.2 - VHIR, Barcelona)

  1. 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. 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
  3. 3. 3 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.
  4. 4. 4 http://galaxyproject.org
  5. 5. 5 Galaxy Conceptual Framework
  6. 6. 66 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. 7. 77 Getting Data Click Get Data
  8. 8. 88 Getting Data: Table Browser Get Table Main
  9. 9. 99 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
  10. 10. 1010 Getting Data: Upload File Upload File Execute File Format Species Upload or paste file
  11. 11. 11 Getting Data: Upload File Specify multiple URLs into the "URL / Text" box
  12. 12. 12 • 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
  13. 13. 13 Text Manipulation Tools
  14. 14. 14 Filter and Sort
  15. 15. 15 Operate on Genomic Intervals
  16. 16. 16 Fasta Manipulation
  17. 17. 1717 Analyzing Data: Next Generation Sequencing
  18. 18. 18 Analyzing Data: Next Generation Sequencing FASTQ file manipulation, like format conversation, summary statistics, trimming reads, filtering reads by quality score…
  19. 19. 19 Analyzing Data: Next Generation Sequencing Input: sanger FASTQ Output: SAM format
  20. 20. 20 Analyzing Data: Next Generation Sequencing
  21. 21. 21 • 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. 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
  23. 23. 23 Workflow Creates a workflow, allows user to repeat analysis using different datasets.
  24. 24. 24 • 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

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