Difference between revisions of "Edgenl2g"
| Line 33: | Line 33: | ||
* tabix | * tabix | ||
| − | = Detailed Contents = | + | = Detailed Contents Part One: Linux = |
== The command <code>ls</code> lists files and subdirectories in a directory== | == The command <code>ls</code> lists files and subdirectories in a directory== | ||
== The command <code>man</code> provides help for a command == | == The command <code>man</code> provides help for a command == | ||
| Line 59: | Line 59: | ||
=== FASTQ on the command line === | === FASTQ on the command line === | ||
=== Using paste to manipulate fastq === | === 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== | ||
Revision as of 17:43, 2 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
