Informatics for RNA-Seq Analysis 2016

Workshop pages for students

This workshop refers to content in the RNA-Seq wiki.

Course Schedule

Schedule for June 16 to June 17, 2016

Workshop Q/A Forum

Post your workshop questions here!


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Class Photo

class photo

Laptop Setup Instructions

Instructions to setup your laptop can be found here.

Difference Between R and RStudio

RStudio doesn’t know where libraries are installed, when they are not installed through the RStudio package manager. To tell RStudio the location, you can define the path in a startup file. Create a file called .Renviron . Inside there:

R_LIBS=<R Library Path of other installed packages>

That was the problem when students installed things in RStudio at the command line using the R command install.package().

… or you could use the package manger to install libraries.

Syntax highlighting

… of scripts in the R editor does not seem to work under Windows. If you want highlighted syntax, use RStudio instead.

Pre-workshop Readings

Before coming to the workshop read these:

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

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

4) Sequencing Terminology

Logging into the Amazon Cloud

Instructions can be found here.

  • We have set up 32 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.

YouTube Playlist for Recorded Lectures

Recorded Lectures’ Playlist

R Review Session

Fouad Yousif



Day 1


Ann Meyer

Module 0: Introduction to Cloud Computing

Obi Griffith


Recorded Lecture

Module 1: Introduction to RNA Sequencing and Analysis

Malachi Griffith


Recorded Lecture

Module 1 Lab

Lab practical


Reference Genomes




Data QC

Module 2: RNA-Seq Alignment and Visualization

Fouad Yousif


Recorded Lecture

Module 2 Lab

Lab practical

Adapter Trim



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

Day 2

Module 3: Expression and Differential Expression

Obi Griffith


Recorded Lecture

Module 3 Lab

Lab practical


Differential Expression

DE Visualization

Module 4: Isoform Discovery and Alternative Expression

Malachi Griffith


Recorded Lecture

Module 4 Lab

Lab Practical

Ref Guided

De novo


Differential Splicing

Splicing Visualization

Module 5: Reference Free Alignment

Obi Griffith


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

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

Data for the Workshop

Tool Installation

Instructions for installing the tools used in the workshops can be found here.

Results from Instructor’s Instance on Amazon

View on GitHub