High-throughput Biology: From Sequence to Networks 2015 New

Course Objectives

With the introduction of next generation sequencing platforms, it is becoming feasible to consider sequencing approaches to address many research projects. Now more than ever, having knowledge of the available bioinformatic resources and the informatic skills to analyze such data is critical.

The Canadian Bioinformatics Workshops, in collaboration with Cold Spring Harbor and New York Genome Center, has developed a comprehensive 7-day course covering the key bioinformatics concepts and tools required to analyze DNA- and RNA-sequence reads using a reference genome. Participants will gain experience in cloud computing and data visualization tools, which will be applied throughout the course. Beginning with an understanding of the workflow involved to move from platform images to sequence generation, participants will gain practical experience and skills to be able to evaluate sequence read quality, map reads to a reference and analyze sequence reads for variation and expression level. The workshop will conclude with analyzing and conducting pathway and network analysis on the resultant ‘gene’ list. The tutorials are designed as self-contained units that include example data (e.g. Illumina paired-end data) and detailed instructions for installation of all required bioinformatics tools.

Course Material

Open Access LogoCanadian Bioinformatics Workshops promotes open access. Past workshop content is available under a Creative Commons License.

Module 1 - Introduction to HT-seq and Cloud Computing (CSHL - 2015) (Faculty: Francis Ouellette)

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Module 2 - Genome Alignment (CSHL - 2015) (Faculty: Matei David)

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Module 3 - Genome Visualization (CSHL - 2015) (Faculty: Marc Fiume)

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Module 4 - De Novo Assembly (CSHL - 2015) (Faculty: Jared Simpson)

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Module 5 - Genome Variation (CSHL - 2015) (Faculty: Guillaume Bourque)

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Module 6 - Genome Structural Variation (CSHL - 2015) (Faculty: Guillaume Bourque)

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Module 7 - Bringing it Together with Galaxy (CSHL - 2015) (Faculty: Francis Ouellette)

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Module 8 - Introduction to RNA sequencing and analysis (CSHL - 2015) (Faculty: Malachi Griffith)

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Module 9 - RNA-seq alignment and visualization (CSHL - 2015) (Faculty: Obi Griffith)

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Module 10 - Expression and Differential Expression (CSHL - 2015) (Faculty: Obi Griffith)

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Module 11 - Isoform Discovery and Alternate Expression (CSHL - 2015) (Faculty: Malachi Griffith)

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Module 12 - Introduction to Pathway and Network Analysis (CSHL - 2015) (Faculty: Lincoln Stein)

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Module 13 - Finding Over-represented Pathways in Gene Lists (CSHL - 2015) (Faculty: Quaid Morris)

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Module 14 - Network Visualization and Analysis with Cytoscape (CSHL - 2015) (Faculty: Jüri Reimand)

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Module 15 - More depth on Pathway and Network Analysis (CSHL - 2015) (Faculty: Robin Haw)

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Module 16 - Gene Function Prediction (CSHL - 2015) (Faculty: Quaid Morris)

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Module 17 - Regulatory Network Analysis (CSHL - 2015) (Faculty: Michael Hoffman)

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