High-throughput Biology - From Sequence to Networks 2019

Welcome

Welcome to High-throughput Biology - From Sequence to Networks 2019.

The course schedule can be found here

If you have questions or comments, visit the workshop Q&A forum. You may need to join the group by clicking on the “+” symbol and entering the class code.

You can download the printed course manual here.


Class Photo

Coming soon!


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.

2) UNIX Preparation tutorials:

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:


Day 1

Welcome

Michelle Brazas

Module 1: Introduction to High-throughput Sequencing

Sara Goodwin

Lecture

Lab Practical Lab Practical on GitHub

Module 2: Data Visualization

Heather Gibling

Lecture

Lab Practical
Lab Practical on GitHub

Module 3: Genome Alignment

Mathieu Bourgey

Lecture

Lab Practical: Connecting to the 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.

Lab Practical
Lab Practical on GitHub


Day 2

Module 4: Small-Variant Calling and Annotation

Mathieu Bourgey

Lecture

Lab Practical
Lab Practical on GitHub

Module 5: Structural Variant Calling

Mathieu Bourgey

Lecture

Lab Practical
Lab Practical on GitHub

Module 6: De Novo Assembly

Jared Simpson

Lecture

Lab Practical Lab Practical on GitHub

Supplemental

Integrated Assignment

Integrated Assignment


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

Lab Practical

Installation

Reference Genomes

Annotations

Indexing

Data

Data QC

Module 8: RNA-seq Alignment and Visualization

Obi Griffith

Lecture

Lab Practical

Adapter Trim

Alignment

IGV

Alignment Visualization

Alignment QC

Integrated Assignment

Kelsy Cotto

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

Assignment Questions

Assignment Answers


Day 4

Module 9: Expression and Differential Expression

Obi Griffith

Lecture

Lab Practical

Expression

Differential Expression

DE Visualization

Module 10: Reference Free Alignment

Malachi Griffith

Kallisto

Module 11: Isoform Discovery and Alternative Expression

Kelsy Cotto

Lecture

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


Day 5

Module 12: Introduction to Pathway and Network Analysis

Jüri Reimand

Lecture

Module 13: Finding Over-Represented Pathways

Jüri Reimand

Lecture

Module 13 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 and Reactome

Robin Haw

Lecture Part 1

Lecture Part 2

Module 14 Lab Practical: De novo subnetwork clustering analysis - Reactome

Robin Haw

Lab Practical 1

Lab Practical 2


Day 6

Module 15: More Depth on Network and Pathway Analysis and Cytoscape Enrichment map

Veronique Voisin

Lecture

Module 15 Lab Practical: Cytoscape-Enrichment Map

Lecture

Lab Practical

Lab answers

Module 16: Gene Function Prediction

Quaid Morris

Lecture

Lab Practical


Day 7

Module 17: Regulatory Network Analysis

Michael Hoffman

Lecture

Module 17 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

Integrated Assignment

Integrated Assignment

Integrated Assignment Answers