Informatics for RNA-Seq Analysis 2015

Laptop Setup Instructions

Instructions for setting up your laptop can be found here: Laptop Setup Instructions

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 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) IGV Tutorial: Review how to use IGV Genome Browser if you have not used this tool before.

• The IGV Tutorial

Pre-Workshop Readings

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

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

Logging into the Amazon cloud

Instructions can be found here.

R Review Session

RNA-seq2015_RReview.pdf
RNA-seq2015_RReviewScripts.R

Day 1

Welcome

Module 0: Introduction to cloud computing

Lecture slides:
RNASeq_Module0_AmazonPreTutorial.pdf RNASeq_Module0_AmazonPreTutorial.ppt](https://bioinformatics.ca/rnaseq2015module1pptx-0)
RNASeq_Module0_AmazonPreTutorial.mp4](https://bioinformatics.ca/rnaseq2015module1mp4)

Module 1: Introduction to RNA sequencing and analysis

Lecture slides:

RNASeq_Module1_Lecture.pdf
RNASeq_Module1_Lecture.ppt
RNASeq_Module1_Lecture.mp4

Lab introduction slides:

RNASeq_Module1_Tutorial.pdf

Lab practical:

http://www.rnaseq.wiki - Module 1 Tutorial

Module 2: RNA-seq alignment and visualization

Lecture slides:

RNASeq_Module2_Lecture.pdf
RNASeq_Module2_Lecture.ppt
RNASeq_Module2_Lecture.mp4

Lab introduction slides:

RNASeq_Module2_Tutorial.pdf

Lab practical:

http://www.rnaseq.wiki - Module 2 Tutorial

Integrated Assignment - Day 1

Paper for Integrated Assignment:

Recurrent chimeric RNAs enriched in human prostate cancer identified by deep sequencing PMC3107329

Assignment Questions:

Integrated Assignment

Answer Key:

Integrated Assignment Answers

Day 2

Module 3: Expression and Differential Expression

Lecture slides:

RNASeq_Module3_Lecture.pdf
RNASeq_Module3_Lecture.ppt
RNASeq_Module3_Lecture.mp4

Lab introduction slides:

RNASeq_Module3_Tutorial.pdf

Lab practical:

http://www.rnaseq.wiki - Module 3 Tutorial

Module 4: Isoform discovery and alternative expression

Lecture slides:

RNASeq_Module4_Lecture.pdf
RNASeq_Module4_Lecture.ppt
RNASeq_Module4_Lecture.mp4

Lab introduction slides:

RNASeq_Module4_Tutorial.pdf

Lab practical:

http://www.rnaseq.wiki - Module 4 Tutorial

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

For additional resources, tutorials, future directions, and more please refer to the RNA-seq wiki: http://www.rnaseq.wiki

Tools with installation instruction in our Amazon server

https://github.com/griffithlab/rnaseq_tutorial/wiki/Installation

Data Sets from Workshop

* RNA-seq Integrated Data
* RNA-seq Integrated Reference

Results from Instructor’s Instance on Amazon

* RNA-seq result

Launching CBW AMI

Steps to launch CBW public AMI

• AMI ID: ami-b9a253d2
• AMI Name: CBW workshops 2015