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!
Survey
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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
Methods to study splicing from high-throughput RNA sequencing data
Differential analysis of gene regulation at transcript resolution with RNA-seq
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.
- 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
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
R Review Session
Fouad Yousif
Day 1
Welcome
Ann Meyer
Module 0: Introduction to Cloud Computing
Obi Griffith
Module 1: Introduction to RNA Sequencing and Analysis
Malachi Griffith
Module 1 Lab
Module 2: RNA-Seq Alignment and Visualization
Fouad Yousif
Module 2 Lab
Integrated Assignment
Fouad Yousif
Paper: Recurrent chimeric RNAs enriched in human prostate cancer identified by deep sequencing
Day 2
Module 3: Expression and Differential Expression
Obi Griffith
Module 3 Lab
Module 4: Isoform Discovery and Alternative Expression
Malachi Griffith
Module 4 Lab
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.