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Syntax
#1-ii. 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.
| Previous Section | This Section | Next Section | |:----------------------------:|:------------------------:|:------------------------------------------:| | Authors | Syntax | Logging into Amazon Cloud |
Table of Contents
Module 1: Authors | Syntax | Logging into Amazon Cloud | Environment | Resources
Module 2: Installation | Reference Genomes | Annotations | Indexing | Data | Data QC
Module 3: Alignment | Alignment Visualization | Alignment QC
Module 4: Expression | Differential Expression | DE Visualization
Module 5: Ref Guided | De novo | Merging | Differential Splicing | Splicing Visualization
Appendix: AWS Setup | Assignment Solutions