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

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

    • 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 • 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 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 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 the menus and data will appear show you the history of your analysis steps, allow you view data and results, and more. RegisterUser
    • 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: UCSC Genes table: knownGene region: position, chrX Output format: BED, and check Send output to Galaxy
    • 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 – Text Manipulation tools – Filter and Sort – Operate on Genomic Intervals – Quality Control – Mapping Data • History and workflow • Galaxy Exercises NGS Analysis Using 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, trimming reads, filtering reads by quality score…
    • 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 – Quality Control – Mapping Data • History and workflow • Galaxy Exercises NGS Analysis Using Galaxy
    • 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 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 – Quality Control – Mapping Data • History and workflow • Galaxy Exercises NGS Analysis Using Galaxy