High-throughput Biology - From Sequence to Networks 2019

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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.

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Class Photo

Link to all class photos

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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:

• 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

• Informatics for RNA Sequencing: A Web Resource for Analysis on the Cloud

• Transcript-level expression analysis of RNA-seq experiments with HISAT, StringTie and Ballgown

• ENCODE RNA-Seq Standards

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

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

• De novo transcript sequence reconstruction from RNA-seq using the Trinity platform for reference generation and analysis

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

• Pathway enrichment analysis and visualization of omics data using g:Profiler, GSEA, Cytoscape and EnrichmentMap

• 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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Day 1

Welcome

Michelle Brazas

Module 1: Introduction to High-throughput Sequencing

Sara Goodwin

Lecture

Module 2: Data Visualization

Heather Gibling

Lecture

Lab Practical

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.

• Detail instructions can be found here.

Lab Practical

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Day 2

Module 4: Small-Variant Calling and Annotation

Mathieu Bourgey

Lecture

Lab Practical

Module 5: Structural Variant Calling

Mathieu Bourgey

Lecture

Lab Practical

Module 6: De Novo Assembly

Jared Simpson

Lecture

Lab Practical

Supplemental

Interesting paper on gaps: Mind the gaps - ignoring errors in long read assemblies critically affects protein prediction

Integrated Assignment - Day 2

Heather Gibling

Integrated Assignment

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Day 3

Day 3 and Day 4 refer to content on rnabio.org.

Module 7: Introduction to RNA Sequencing Analysis

Malachi Griffith

Lecture

Module 7 Lab Practical

Malachi Griffith

Installation

Reference Genomes

Annotations

Indexing

Data

Data QC

Module 8: RNA-seq Alignment and Visualization

Christopher Miller

Lecture

Module 8 Lab Practical

Christopher Miller

Adapter Trim

Alignment

Alignment Visualization

Alignment QC

IGV

Integrated Assignment - Day 3

Kelsy Cotto

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

Christopher Miller

Lecture

Module 9 Lab Practical

Christopher Miller

Expression

Differential Expression

DE Visualization

Module 10: Reference Free Alignment

Malachi Griffith

Lecture

Module 10 Lab Practical

Malachi Griffith

Kallisto

Module 11: Isoform Discovery and Alternative Expression

Kelsy Cotto

Lecture

Module 11 Lab Practical

Kelsy Cotto

Ref Guided

De novo

Merging

Differential Splicing

Splicing Visualization

Integrated Assignment - Day 4

Kelsy Cotto

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 tutorial

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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

Lab Practical

Genelist_GBM.txt

Genelist_KIRC.txt

hsapiens.pathways.NAME.gmt

Module 14: Network Visualization and Analysis with Cytoscape and Reactome

Robin Haw

Lecture Part 1

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

Robin Haw

Lab Practical Slides

Lab Practical Exercises

Integrated Assignment - Day 5

Veronique Voisin

Slides

Integrated Assignment

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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

Veronique Voisin

Lab Practical - Part 1

Lab Practical - Part 2

Lab Practical - Part 3 Optional

Module 16: Gene Function Prediction

Quaid Morris

Lecture

Lab Practical - web version

Lab Practical - Cytoscape version

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Day 7

Module 17: Regulatory Network Analysis

Michael Hoffman

Lecture

Lecture with missing animation

Module 17 Lab Practical: iRegulon

Veronique Voisin

Lab lecture

Lab practical

Precomputed results cys file

Precomputed results irf file

Integrated Assignment - Day 7

Veronique Voisin

Integrated Assignment

Integrated Assignment Answers

Post Workshop

Post workshop content for data sets, docker containers, AWS image, tools and install instructions can be found here

Additional resources for continuing your bioinformatics education can be found here