week_08

Week 8

RNAseq Part 2

• Lecture Recording

• Abundance Estimation 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 in last week lecture

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

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

Complete Expression Analysis portion of Module 3 - Expression

For-credit students: please find the TPM value of gene CECR7 in sample HBR_Rep1 and send that to Jenny.