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Syntax
In this tutorial, created using Github Flavored Markdown, fenced code blocks are commands necessary to complete the tutorial. Some sections are marked as optional and can be skipped.
A fenced code block will look like this:
sudo apt-get install tree
cd ~
# comment
tree -I workspace/tools
All lines contained within the highlighted boxes will need to be executed at the command line. When copy/paste is used be sure to hit Return or Enter after pasting each command or set of commands. All lines starting with a '#' are comments and will not be interpretted by the shell.
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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