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UNIX Tutorial
###Introduction
UNIX is a command line operating system (OS)
- It is the backbone of popular graphical OS's like Apple's OS X and Linux
Unix is built on a simple modular philosophy
- UNIX is based on files and processes. In other words, all the OS 'sees' are files and processes even though there are directories and other types, they are all viewed by the OS as a file. This is useful as it makes it easier to pass files around the system.
- The OS provides a unified filesystem to facilitate communication between programs
- The OS operates on a set of simple programs that each provide a single well defined function.
###The Kernel
The kernel is the hub of the OS. It does all of the work behind the scenes.
- The kernel executes programs
- Allocates time and memory to programs
###The shell
The shell is the interface between the kernel and the user.
- Is a command line interpreter -- It has a defined syntax to execute processes
- Can be customized to user preferences
- Provides shortcuts for usability (tab completion)
- Stores a history of all commands run. Try
historyor press the up arrow in the terminal
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