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Environment
#0-vi. Environment This tutorial assumes use of a Linux computer with an 'x86_64' architecture. The rest of the tutorial should be conducted in a linux Terminal session. In other words you must already be logged into the Amazon EC2 instance as described in the previous section.
Before proceeding you must define a global working directory by setting the environment variable: 'RNA_HOME'
Log into a server and SET THIS BEFORE RUNNING EVERYTHING.
Create a working directory and set the 'RNA_HOME' environment variable
mkdir -p ~/workspace/rnaseq/
export RNA_HOME=~/workspace/rnaseq
Make sure whatever the working dir is, that it is set and is valid
echo $RNA_HOME
You can place the RNA_HOME variable in your .bashrc and then logout and login again to avoid having to worry about it. This has been done for you in the pre-configured amazon instance that you will be using.
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##Note: The current version of this tutorial is now at www.rnaseq.wiki
Table of Contents
Module 0: Authors | Citation | Syntax | Intro to AWS | Log into AWS | Unix | Environment | Resources
Module 1: Installation | Reference Genomes | Annotations | Indexing | Data | Data QC
Module 2: Adapter Trim | Alignment | IGV | Alignment Visualization | Alignment QC
Module 3: Expression | Differential Expression | DE Visualization
Module 4: Ref Guided | De novo | Merging | Differential Splicing | Splicing Visualization
Module 5: Kallisto
Appendix: Abbreviations | Lectures | Practical Exercise Solutions | Integrated Assignment | Proposed Improvements | AWS Setup