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Syntax
#Syntax
In Github Flavored Markdown, fenced code blocks are optional portions of the tutorials where as indented code blocks are required to complete the tutorial.
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.
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