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Syntax
#0-iii. Syntax
In this tutorial, created using Github Flavored Markdown, fenced code blocks are optional portions of the tutorials whereas indented code blocks are required to complete the tutorial.
A fenced code block will look like this:
sudo apt-get install tree
cd ~
tree -I tools
An indented code block will look very similar in the wiki but will be interpreted differently when this tutorial is parsed:
sudo apt-get install tree
cd ~
tree -I tools
To make the Markdown files bash/shell compatible, a script will add a comment or '#' character to all lines that are NOT indented with a TAB character.
In text form, all lines starting with a '#' are comments and will not be executed. Therefore, fenced code blocks will be ignored when converted to a bash script.
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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