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Environment
#ENVIRONMENT
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.
You can then PLACE IT IN YOUR .bashrc and then logout and login again to avoid having to worry about it
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
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