Difference between revisions of "Edgenl2g"
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* 2/3's core linux 1/3 genomics focus | * 2/3's core linux 1/3 genomics focus | ||
| − | = Contents = | + | = General Contents = |
== Core Linux == | == Core Linux == | ||
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* Files and directories | * Files and directories | ||
* Navigating the file system | * Navigating the file system | ||
| − | * File management | + | * File management* |
* Permissions | * Permissions | ||
* Accessing files | * Accessing files | ||
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* bedtools | * bedtools | ||
* tabix | * tabix | ||
| + | |||
| + | = Detailed Contents Part One: Linux = | ||
| + | == The command <code>ls</code> lists files and subdirectories in a directory== | ||
| + | == The command <code>man</code> provides help for a command == | ||
| + | == Basic Linux/Unix tips for filenames== | ||
| + | == Changing directories == | ||
| + | == Tab completion for commands and filenames== | ||
| + | == Command history == | ||
| + | == Making and removing (empty) directories== | ||
| + | == Text editors == | ||
| + | == Reading text files== | ||
| + | == Copying files == | ||
| + | == Removing directories == | ||
| + | == Piping and outputting to files == | ||
| + | == Grep == | ||
| + | == What permissions mean == | ||
| + | == Head and tail == | ||
| + | == Redirection == | ||
| + | == Working with zipped data == | ||
| + | == Some other useful information == | ||
| + | === Stopping processes === | ||
| + | === Clearing the terminal === | ||
| + | === Copying and pasting text === | ||
| + | == Environment Variables== | ||
| + | == The FASTQ format == | ||
| + | === FASTQ on the command line === | ||
| + | === Using paste to manipulate fastq === | ||
| + | === awk for data in columns === | ||
| + | === FASTQ to FASTA conversion === | ||
| + | == Process Management == | ||
| + | == Simple shell scripts == | ||
| + | == If you finish and you are bored == | ||
| + | |||
| + | = Detailed Contents Part Two: Command-line tools for Genomics = | ||
| + | |||
| + | == bedtools == | ||
| + | ==seqtk== | ||
| + | ==samtools== | ||
| + | == Bioawk== | ||
Latest revision as of 12:09, 3 October 2016
Contents
- 1 Introduction
- 2 General Contents
- 3 Detailed Contents Part One: Linux
- 3.1 The command ls lists files and subdirectories in a directory
- 3.2 The command man provides help for a command
- 3.3 Basic Linux/Unix tips for filenames
- 3.4 Changing directories
- 3.5 Tab completion for commands and filenames
- 3.6 Command history
- 3.7 Making and removing (empty) directories
- 3.8 Text editors
- 3.9 Reading text files
- 3.10 Copying files
- 3.11 Removing directories
- 3.12 Piping and outputting to files
- 3.13 Grep
- 3.14 What permissions mean
- 3.15 Head and tail
- 3.16 Redirection
- 3.17 Working with zipped data
- 3.18 Some other useful information
- 3.19 Environment Variables
- 3.20 The FASTQ format
- 3.21 Process Management
- 3.22 Simple shell scripts
- 3.23 If you finish and you are bored
- 4 Detailed Contents Part Two: Command-line tools for Genomics
Introduction
Details of Edinburgh Genomics' Linux for Genomics course
Duration
- 1 day
- 2/3's core linux 1/3 genomics focus
General Contents
Core Linux
- The shell and commands
- Getting help
- Files and directories
- Navigating the file system
- File management*
- Permissions
- Accessing files
- Downloading remote files
- Zipping and unzipping files
- Pipes and redirects
- Filtering / manipulating file content
- Shell scripts
- Process management
Focused Genomics
Command-line tools for genomics
- seqtk
- bioawk
- samtools
- bedtools
- tabix
