High-Throughput Biology - From Sequence to Networks 2017

Welcome

Welcome to High-Throughput Biology: From Sequence to Networks.

The course schedule can be found here.

If you have questions or comments, visit the workshop Q&A forum.

We value your feedback. Please complete our survey.

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Pre-Workshop Materials

Laptop Setup Instructions

Instructions to setup your laptop can be found here.

Pre-workshop Tutorials

1) R Preparation tutorials: You are expected to have completed the following tutorials in R beforehand. The tutorial should be very accessible even if you have never used R before.

• The CBW R tutorial
• Quick and Dirty Guide to R
• The R Tutorial up to and including 5. Basic Plots
• The R command cheat sheet

2) UNIX Preparation tutorials:

• UNIX Bootcamp
• Tutorials #1-3 on UNIX Tutorial for Beginners
• Unix Cheat sheet

3) Sequencing Terminology

4) Cytoscape Preparation tutorials: Complete the introductory tutorial to Cytoscape

• Introduction to Cytoscape3 - User Interface

• Introduction to Cytoscape3 - Welcome Screen

• Filtering and Editing in Cytoscape 3

Pre-workshop Readings

Before coming to the workshop, read these:

• Using cloud computing infrastructure with CloudBioLinux, CloudMan, and Galaxy

• Integrative Genomics Viewer (IGV): high-performance genomics data visualization and exploration

• Genome structural variation discovery and genotyping

• A survey of sequence alignment algorithms for next-generation sequencing

• Genotype and SNP calling from next-generation sequencing data

• Differential gene and transcript expression analysis of RNA-seq experiments with TopHat and Cufflinks

• ENCODE RNA-Seq Standards

• Methods to study splicing from high-throughput RNA sequencing data

• Differential analysis of gene regulation at transcript resolution with RNA-seq

• A comprehensive assessment of RNA-seq accuracy, reproducibility and information content by the Sequencing Quality Control Consortium

• Recurrent chimeric RNAs enriched in human prostate cancer identified by deep sequencing

• iRegulon: From a Gene List to a Gene Regulatory Network Using Large Motif and Track Collections

• The GeneMANIA prediction server: biological network integration for gene prioritization and predicting gene function

• GeneMANIA Prediction Server 2013 Update

• How to visually interpret biological data using networks

• g:Profiler–a web-based toolset for functional profiling of gene lists from large-scale experiments

• g:Profiler–a web server for functional interpretation of gene lists (2011 update)

• Gene set enrichment analysis: a knowledge-based approach for interpreting genome-wide expression profiles

• Expression data analysis with reactome

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Logging into the Amazon Cloud

• We have set up 30 instances on the Amazon cloud - one for each student. In order to log in to your instance, you will need a security certificate. If you plan on using Linux or Mac OS X, please download this certificate. Otherwise if you plan on using Windows (with Putty and Winscp), please download this certificate.

• Detail instructions can be found here.

Day 1

Welcome

Ann Meyer

Module 1: Introduction to High-throughput Sequencing

Jared Simpson

Lecture

Recording

Module 2: Data Visualization

Florence Cavalli

Lecture

Recording

Lab Practical

Module 3: Genome Alignment

Mathieu Bourgey

Lecture

Recording

Lab Practical: Connecting to the Cloud

Lecture

• We have set up 30 instances on the Amazon cloud - one for each student. In order to log in to your instance, you will need a security certificate. If you plan on using Linux or Mac OS X, please download this certificate. Otherwise if you plan on using Windows (with Putty and Winscp), please download this certificate.

Lab Practical
Lab Practical on GitHub

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Day 2

Module 4: Small-Variant Calling and Annotation

Mathieu Bourgey

Lecture

Recording

Lab Practical
Lab Practical on GitHub

Module 5: Structural Variant Calling

Mathieu Bourgey

Lecture

Recording

Lab Practical
Lab Practical on GitHub

Module 6: De Novo Assembly

Jared Simpson

Lecture

Recording

Lab Practical

Supplemental

Integrated Assignment

Integrated Assignment

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Day 3

Day 3 and Day 4 refer to content in the RNA-Seq wiki.

Module 7: Introduction to RNA Sequencing Analysis

Malachi Griffith

Lecture

Recording

Lab Practical

Lab practical

Installation

Reference Genomes

Annotations

Indexing

Data

Data QC

Module 8: RNA-seq Alignment and Visualization

Fouad Yousif

Lecture

Recording

Lab Practical

Lab Practical

Adapter Trim

Alignment

IGV

Alignment Visualization

Alignment QC

Integrated Assignment

Fouad Yousif

Paper: Recurrent chimeric RNAs enriched in human prostate cancer identified by deep sequencing

Assignment Questions

Assignment Answers

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Day 4

Module 9: Expression and Differential Expression

Obi Griffith

Lecture

Recording

Lab Practical

Lab Practical

Expression

Differential Expression

DE Visualization

Module 10: Reference Free Alignment

Malachi Griffith

Kallisto

Module 11: Isoform Discovery and Alternative Expression

Malachi Griffith

Lecture

Recording

Lab Practical

Lab Practical

Ref Guided

De novo

Merging

Differential Splicing

Splicing Visualization

Integrated Assignment

Assignment Questions

Assignment Answers

Keeping Up-to-date with RNA-Seq Analysis Developments

For additional resources, tutorials, future directions, and more please refer to the RNA-seq wiki

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Day 5

Module 12: Introduction to Pathway and Network Analysis

Jüri Reimand

Lecture

Recording

Module 13: Finding Over-Represented Pathways

Jüri Reimand

Lecture

Recording

Lab practical: Enrichment-Based Analysis - Performing ORA

Jüri Reimand and Veronique Voisin

Introduction

gProfiler

Exercise 1

Precomputed results for exercise 1

GSEA Exercise 2

Precomputed results for Exercise 2

Module 14: Network Visualization and Analysis with Cytoscape

Veronique Voisin

Lecture Part 1

Lecture Part 2

Recording

Lab practical: Cytoscape Demo, Enrichment Map

Veronique Voisin

Exercise 1

Exercise 2

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Day 6

Module 15: More Depth on Network and Pathway Analysis

Robin Haw

Lecture

Recording

Lab practical: De Novo Subnetwork Clustering Analysis in Reactome

Lecture

Lab Practical

Lab answers

Module 16: Gene Function Prediction

Quaid Morris

Lecture

Recording

Lab Practical

Integrated Assignment

Integrated Assignment

Integrated Assignment Answers

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Day 7

Module 17: Regulatory Network Analysis

Michael Hoffman

Lecture

Recording

Lab practical: iRegulon

Veronique Voisin

Lab lecture

Lab practical

Precomputed results cys file and Precomputed results irf file

To use the precomputed results:

1) launch Cytoscape

2) open the “prostate_cancer_genemania_network.cys” file

3) go to App > iRegulon > ‘Load results from the iregulon_results.irf file’

Download a zip file of the git repo here