week_09

Week 9

RNAseq Part 3

• Lecture Recording

• Differential Expression Slides

• RNA-seq Bioinformatics

RNAseq Course Setup

For the BFX Workshop, we will not be using AWS Cloud. Instead, we will use a Docker image created from the AWS AMI used in rnabio.org.

Docker Setup

Instructions for setting up docker can be found here

User Setup

Reminder: Now that we are running a Docker container, Docker, by default, will log you in as the "root" user. We need to run as the ubuntu user to match the RNAseq course tutorials.

1. Switch User su to the unbutu user:

su ubuntu

2. Source the pre-installed .bashrc file to configure your environment to match the RNAseq course:

source ~/.bashrc

3. Set the environment variable

export RNA_HOME=~/workspace/rnaseq

NOTE: Using Docker and the persistent "workspace" volume we attached will allow you to start/stop as you wish. EVERYTIME YOU LOGIN TO THE DOCKER CONTAINER, YOU MUST LOGIN AS THE ubuntu USER AND source ~/.bashrc UPON EACH LOGIN.

Homework Assignments

Start with Differential Expression Ballgown, and continue through the pages, finishing with "DE Visualization Advanced".

For-credit students

Please provide a screenshot of a volcano plot representing the differentially expressed genes in the dataset. Set the p-value cutoff to 0.01 and the log fold change threshold to 2. Send it to Jenny, as usual.