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Environment
#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.
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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NOTICE: This resource has been moved to rnabio.org. The version here will be maintained for legacy use only. All future development and maintenance will occur only at rnabio.org. Please proceed to rnabio.org for the current version of this course.
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: Alignment Free - Kallisto
Module 5: Ref Guided | De novo | Merging | Differential Splicing | Splicing Visualization
Module 6: Trinity
Module 7: Trinotate
Appendix: Saving Results | Abbreviations | Lectures | Practical Exercise Solutions | Integrated Assignment | Proposed Improvements | AWS Setup