SlideShare ist ein Scribd-Unternehmen logo

BITS: Introduction to Linux - Text manipulation tools for bioinformatics

•Als PPT, PDF herunterladen•
•
BITS
BITS

The document provides an introduction to using the Linux command line for bioinformatics tasks. It covers navigating the file system, manipulating files and directories, input/output redirection, piping commands together, and commonly used text processing tools. The goal is to help users easily use command line tools, automate repetitive tasks, and parse/summarize text-based outputs.

BildungTechnologie
1 von 85
Linux for Bioinformatics ,[object Object],[object Object],[object Object],[object Object],[object Object],BITS/VIB Bioinformatics Training – version 2 – Joachim Jacob Okt 2011 – Luc Ducazu <luc@daphnia.com>
Schedule ,[object Object],[object Object],http://projects.gnome.org/tomboy/
GOAL ,[object Object],[object Object],[object Object],[object Object]
Connecting to Linux ,[object Object],[object Object],[object Object],[object Object],[object Object],[object Object],[object Object],[object Object]
And there we are... username Machine name location
Navigation ,[object Object],[object Object]
The File System Tree / bin boot dev etc home media root sbin tmp usr var james bin sbin share bin sbin share local lib log mail run spool tmp Aka ~ (for james) The variable PATH contains the paths of the bin folders. See command env.
UNIX philosophy ,[object Object],[object Object],[object Object],[object Object],[object Object]
Names of files & directories ,[object Object],[object Object],[object Object],[object Object],[object Object],[object Object]
Navigation in the shell ,[object Object],[object Object]
Navigation ,[object Object],[object Object],[object Object],[object Object],[object Object],[object Object]
Navigation ,[object Object],[object Object],[object Object],[object Object],[object Object],[object Object],[object Object],[object Object],[object Object],[object Object],[object Object],[object Object],[object Object],[object Object],[object Object],[object Object],[object Object]
Exercise ,[object Object],[object Object]
Exploration ,[object Object],[object Object],[object Object],[object Object],[object Object],[object Object],[object Object],[object Object],[object Object]
Exploration ,[object Object],[object Object]
Exploration ,[object Object],[object Object],[object Object],[object Object],[object Object],[object Object],[object Object]
Exploring text files ,[object Object],[object Object],[object Object]
Conquest of the file system ,[object Object],[object Object],[object Object],[object Object],[object Object],[object Object],[object Object],[object Object]
Creating directories ,[object Object],[object Object],[object Object],[object Object]
Creating directories ,[object Object],[object Object],[object Object],[object Object],[object Object],[object Object]
Removing directories ,[object Object],[object Object],[object Object]
Creating a file ,[object Object],[object Object],[object Object],[object Object],[object Object],[object Object],[object Object],[object Object]
Creating a file ,[object Object],[object Object],[object Object],[object Object],[object Object],[object Object],[object Object],[object Object],[object Object]
Copying files ,[object Object],[object Object],[object Object]
Copying files ,[object Object],[object Object],[object Object],[object Object],[object Object],[object Object],[object Object],[object Object]
Moving / renaming files ,[object Object],[object Object],[object Object]
Removing files ,[object Object],[object Object],[object Object],[object Object],[object Object],[object Object],[object Object]
Remotely copying files ,[object Object],[object Object],[object Object],[object Object],Command to copy username machine Path to the remote folder / file you want to copy To the local current dir
Exercise ,[object Object],[object Object],[object Object],[object Object]
Solutions ,[object Object],[object Object],[object Object],[object Object],[object Object],[object Object],[object Object],[object Object]
Exercise ,[object Object],[object Object],[object Object],[object Object],[object Object],[object Object],[object Object],[object Object]
Executables ,[object Object],[object Object],[object Object],[object Object],[object Object],[object Object],[object Object],[object Object],[object Object],[object Object]
Exercise ,[object Object],[object Object],[object Object],[object Object],[object Object],[object Object],[object Object]
Advanced ,[object Object],[object Object],[object Object],[object Object],[object Object],[object Object],[object Object],[object Object]
Which programs are running
Which programs are running
Which programs are running
Which programs are running
Which programs are running
I/O redirection of terminal programs ,[object Object],[object Object],[object Object],[object Object],[object Object],[object Object],[object Object],[object Object],[object Object],[object Object]
I/O redirection ,[object Object],[object Object],[object Object],[object Object],[object Object]
I/O redirection ,[object Object],[object Object]
Input redirection ,[object Object],[object Object],[object Object],[object Object],[object Object],Emailing tool Option to set the subject recipient Content is read from file
Output redirection ,[object Object],[object Object],[object Object]
Output redirection ,[object Object],[object Object]
Error redirection ,[object Object]
Special devices ,[object Object],[object Object],[object Object],[object Object],[object Object],[object Object]
Playing with out- and input: pipes ,[object Object],[object Object],[object Object],[object Object],[object Object],[object Object],[object Object]
Compression of files ,[object Object],[object Object],[object Object],[object Object],[object Object]
tar ,[object Object],[object Object],[object Object],[object Object],[object Object],[object Object],[object Object],[object Object],[object Object]
Compression ,[object Object],[object Object],[object Object],[object Object],[object Object],[object Object],[object Object],[object Object]
Decompression ,[object Object],[object Object],[object Object],[object Object],[object Object]
Text tools ,[object Object],[object Object],[object Object],[object Object],[object Object],[object Object],[object Object],[object Object],[object Object],[object Object]
Exchanging text files ,[object Object],[object Object],[object Object],[object Object]
Regular expressions ,[object Object],[object Object],[object Object],[object Object]
grep ,[object Object],[object Object],[object Object]
grep ,[object Object],[object Object],[object Object],[object Object],[object Object],[object Object],[object Object],[object Object]
grep ,[object Object],[object Object]
Exercise ,[object Object],[object Object],[object Object],[object Object],[object Object]
Solution ,[object Object],[object Object]
Word Count ,[object Object],[object Object],[object Object],[object Object],[object Object],[object Object]
Transform ,[object Object],[object Object],[object Object],[object Object],[object Object]
Transform ,[object Object],[object Object],[object Object],[object Object]
awk ,[object Object],[object Object],[object Object]
awk (1) ,[object Object],[object Object],[object Object],[object Object],[object Object],[object Object],[object Object],[object Object],[object Object],[object Object]
awk (1) ,[object Object],[object Object],[object Object],[object Object]
awk (2) ,[object Object],[object Object],[object Object],[object Object],[object Object]
awk (2) ,[object Object]
cut ,[object Object],[object Object],[object Object],[object Object],[object Object],[object Object],[object Object],[object Object],[object Object]
cut ,[object Object],[object Object],[object Object]
cut ,[object Object],[object Object],[object Object],[object Object],[object Object]
sort ,[object Object],[object Object],[object Object],[object Object]
sort ,[object Object],[object Object],[object Object],[object Object],[object Object],[object Object]
sort ,[object Object],[object Object]
uniq ,[object Object],[object Object],[object Object],[object Object],[object Object]
Eliminate duplicates ,[object Object],[object Object]
Display unique or duplicate lines ,[object Object],[object Object],[object Object],[object Object],[object Object],[object Object],[object Object],[object Object],[object Object],!
Comparing text files ,[object Object],[object Object]
Comparing text files ,[object Object],[object Object]
Comparing files – GUI (meld)
Exercise ,[object Object],[object Object],[object Object]
Exercises ,[object Object],[object Object],[object Object],[object Object],[object Object],[object Object],[object Object],[object Object],[object Object],[object Object]
Solution ,[object Object],[object Object],[object Object]
links ,[object Object],[object Object],[object Object]
Linux ,[object Object]

Empfohlen

Basic linux commands
Basic linux commandsBasic linux commands
Basic linux commandsShakeel Shafiq
 
Unix command line concepts
Unix command line conceptsUnix command line concepts
Unix command line conceptsArtem Nagornyi
 
Linux intro 4 awk + makefile
Linux intro 4 awk + makefileLinux intro 4 awk + makefile
Linux intro 4 awk + makefileGiovanni Marco Dall'Olio
 
VI editor in unix
VI editor in unix VI editor in unix
VI editor in unix Ahmed Fayyaz
 
Introduction to the linux command line.pdf
Introduction to the linux command line.pdfIntroduction to the linux command line.pdf
Introduction to the linux command line.pdfCesleySCruz
 
Publishing Scientific Results
Publishing Scientific ResultsPublishing Scientific Results
Publishing Scientific ResultsTown Peterson
 
Unix Linux Commands Presentation 2013
Unix Linux Commands Presentation 2013Unix Linux Commands Presentation 2013
Unix Linux Commands Presentation 2013Wave Digitech
 
The Systematic Literature Search
The Systematic Literature SearchThe Systematic Literature Search
The Systematic Literature SearchAndrea
 

Empfohlen

Basic linux commands
Basic linux commandsBasic linux commands
Basic linux commandsShakeel Shafiq
 
Unix command line concepts
Unix command line conceptsUnix command line concepts
Unix command line conceptsArtem Nagornyi
 
Linux intro 4 awk + makefile
Linux intro 4 awk + makefileLinux intro 4 awk + makefile
Linux intro 4 awk + makefileGiovanni Marco Dall'Olio
 
VI editor in unix
VI editor in unix VI editor in unix
VI editor in unix Ahmed Fayyaz
 
Introduction to the linux command line.pdf
Introduction to the linux command line.pdfIntroduction to the linux command line.pdf
Introduction to the linux command line.pdfCesleySCruz
 
Publishing Scientific Results
Publishing Scientific ResultsPublishing Scientific Results
Publishing Scientific ResultsTown Peterson
 
Unix Linux Commands Presentation 2013
Unix Linux Commands Presentation 2013Unix Linux Commands Presentation 2013
Unix Linux Commands Presentation 2013Wave Digitech
 
The Systematic Literature Search
The Systematic Literature SearchThe Systematic Literature Search
The Systematic Literature SearchAndrea
 
Introduction to Linux
Introduction to Linux Introduction to Linux
Introduction to Linux Harish R
 
Linux presentation
Linux presentationLinux presentation
Linux presentationNikhil Jain
 
Unix - An Introduction
Unix - An IntroductionUnix - An Introduction
Unix - An IntroductionDeepanshu Gahlaut
 
ITFT - DOS - Disk Operating System
ITFT - DOS - Disk Operating SystemITFT - DOS - Disk Operating System
ITFT - DOS - Disk Operating SystemBlossom Sood
 
System call
System callSystem call
System callshahadat hossain
 
Shell Scripting in Linux
Shell Scripting in LinuxShell Scripting in Linux
Shell Scripting in LinuxAnu Chaudhry
 
Learning sed and awk
Learning sed and awkLearning sed and awk
Learning sed and awkYogesh Sawant
 
Some basic unix commands
Some basic unix commandsSome basic unix commands
Some basic unix commandsaaj_sarkar06
 
Intro to Linux Shell Scripting
Intro to Linux Shell ScriptingIntro to Linux Shell Scripting
Intro to Linux Shell Scriptingvceder
 
Workshop NGS data analysis - 1
Workshop NGS data analysis - 1Workshop NGS data analysis - 1
Workshop NGS data analysis - 1Maté Ongenaert
 
directory structure and file system mounting
directory structure and file system mountingdirectory structure and file system mounting
directory structure and file system mountingrajshreemuthiah
 
Bash shell scripting
Bash shell scriptingBash shell scripting
Bash shell scriptingVIKAS TIWARI
 
Sed & awk the dynamic duo
Sed & awk the dynamic duoSed & awk the dynamic duo
Sed & awk the dynamic duoJoshua Thijssen
 
Linux Basic Commands
Linux Basic CommandsLinux Basic Commands
Linux Basic CommandsHanan Nmr
 
Ebsco
EbscoEbsco
Ebscoegonzaleso493
 
Linux Presentation
Linux PresentationLinux Presentation
Linux PresentationMuhammad Qazi
 
Introduction to System Calls
Introduction to System CallsIntroduction to System Calls
Introduction to System CallsVandana Salve
 
Linux file system
Linux file systemLinux file system
Linux file systemMd. Tanvir Hossain
 
Comprendre les scripts shell auto-extractible
Comprendre les scripts shell auto-extractibleComprendre les scripts shell auto-extractible
Comprendre les scripts shell auto-extractibleThierry Gayet
 
UNIX/Linux training
UNIX/Linux trainingUNIX/Linux training
UNIX/Linux trainingMichael Olafusi
 
Linux Beginner Guide 2014
Linux Beginner Guide 2014Linux Beginner Guide 2014
Linux Beginner Guide 2014Anthony Le Goff
 
Linux crontab
Linux crontabLinux crontab
Linux crontabTeja Bheemanapally
 

Weitere ähnliche Inhalte

Was ist angesagt?

Introduction to Linux
Introduction to Linux Introduction to Linux
Introduction to Linux Harish R
 
Linux presentation
Linux presentationLinux presentation
Linux presentationNikhil Jain
 
ITFT - DOS - Disk Operating System
ITFT - DOS - Disk Operating SystemITFT - DOS - Disk Operating System
ITFT - DOS - Disk Operating SystemBlossom Sood
 
Shell Scripting in Linux
Shell Scripting in LinuxShell Scripting in Linux
Shell Scripting in LinuxAnu Chaudhry
 
Learning sed and awk
Learning sed and awkLearning sed and awk
Learning sed and awkYogesh Sawant
 
Some basic unix commands
Some basic unix commandsSome basic unix commands
Some basic unix commandsaaj_sarkar06
 
Intro to Linux Shell Scripting
Intro to Linux Shell ScriptingIntro to Linux Shell Scripting
Intro to Linux Shell Scriptingvceder
 
Workshop NGS data analysis - 1
Workshop NGS data analysis - 1Workshop NGS data analysis - 1
Workshop NGS data analysis - 1Maté Ongenaert
 
directory structure and file system mounting
directory structure and file system mountingdirectory structure and file system mounting
directory structure and file system mountingrajshreemuthiah
 
Bash shell scripting
Bash shell scriptingBash shell scripting
Bash shell scriptingVIKAS TIWARI
 
Sed & awk the dynamic duo
Sed & awk the dynamic duoSed & awk the dynamic duo
Sed & awk the dynamic duoJoshua Thijssen
 
Linux Basic Commands
Linux Basic CommandsLinux Basic Commands
Linux Basic CommandsHanan Nmr
 
Introduction to System Calls
Introduction to System CallsIntroduction to System Calls
Introduction to System CallsVandana Salve
 
Comprendre les scripts shell auto-extractible
Comprendre les scripts shell auto-extractibleComprendre les scripts shell auto-extractible
Comprendre les scripts shell auto-extractibleThierry Gayet
 

Was ist angesagt? (20)

Introduction to Linux
Introduction to Linux Introduction to Linux
Introduction to Linux
 
Linux presentation
Linux presentationLinux presentation
Linux presentation
 
Unix - An Introduction
Unix - An IntroductionUnix - An Introduction
Unix - An Introduction
 
ITFT - DOS - Disk Operating System
ITFT - DOS - Disk Operating SystemITFT - DOS - Disk Operating System
ITFT - DOS - Disk Operating System
 
System call
System callSystem call
System call
 
Shell Scripting in Linux
Shell Scripting in LinuxShell Scripting in Linux
Shell Scripting in Linux
 
Learning sed and awk
Learning sed and awkLearning sed and awk
Learning sed and awk
 
Some basic unix commands
Some basic unix commandsSome basic unix commands
Some basic unix commands
 
Intro to Linux Shell Scripting
Intro to Linux Shell ScriptingIntro to Linux Shell Scripting
Intro to Linux Shell Scripting
 
Workshop NGS data analysis - 1
Workshop NGS data analysis - 1Workshop NGS data analysis - 1
Workshop NGS data analysis - 1
 
directory structure and file system mounting
directory structure and file system mountingdirectory structure and file system mounting
directory structure and file system mounting
 
Bash shell scripting
Bash shell scriptingBash shell scripting
Bash shell scripting
 
Sed & awk the dynamic duo
Sed & awk the dynamic duoSed & awk the dynamic duo
Sed & awk the dynamic duo
 
Linux Basic Commands
Linux Basic CommandsLinux Basic Commands
Linux Basic Commands
 
Ebsco
EbscoEbsco
Ebsco
 
Linux Presentation
Linux PresentationLinux Presentation
Linux Presentation
 
Introduction to System Calls
Introduction to System CallsIntroduction to System Calls
Introduction to System Calls
 
Linux file system
Linux file systemLinux file system
Linux file system
 
Comprendre les scripts shell auto-extractible
Comprendre les scripts shell auto-extractibleComprendre les scripts shell auto-extractible
Comprendre les scripts shell auto-extractible
 
UNIX/Linux training
UNIX/Linux trainingUNIX/Linux training
UNIX/Linux training
 

Andere mochten auch

Linux Beginner Guide 2014
Linux Beginner Guide 2014Linux Beginner Guide 2014
Linux Beginner Guide 2014Anthony Le Goff
 
Part 5 of "Introduction to Linux for Bioinformatics": Working the command lin...
Part 5 of "Introduction to Linux for Bioinformatics": Working the command lin...Part 5 of "Introduction to Linux for Bioinformatics": Working the command lin...
Part 5 of "Introduction to Linux for Bioinformatics": Working the command lin...Joachim Jacob
 
Job Automation using Linux
Job Automation using LinuxJob Automation using Linux
Job Automation using LinuxJishnu Pradeep
 
Linux beginner's Workshop
Linux beginner's WorkshopLinux beginner's Workshop
Linux beginner's Workshopfutureshocked
 

Andere mochten auch (6)

Linux Beginner Guide 2014
Linux Beginner Guide 2014Linux Beginner Guide 2014
Linux Beginner Guide 2014
 
Linux crontab
Linux crontabLinux crontab
Linux crontab
 
Part 5 of "Introduction to Linux for Bioinformatics": Working the command lin...
Part 5 of "Introduction to Linux for Bioinformatics": Working the command lin...Part 5 of "Introduction to Linux for Bioinformatics": Working the command lin...
Part 5 of "Introduction to Linux for Bioinformatics": Working the command lin...
 
Job Automation using Linux
Job Automation using LinuxJob Automation using Linux
Job Automation using Linux
 
Processor grafxtron
Processor grafxtronProcessor grafxtron
Processor grafxtron
 
Linux beginner's Workshop
Linux beginner's WorkshopLinux beginner's Workshop
Linux beginner's Workshop
 

Ähnlich wie BITS: Introduction to Linux - Text manipulation tools for bioinformatics

Command Line Tools
Command Line ToolsCommand Line Tools
Command Line ToolsDavid Harris
 
Shell_Scripting.ppt
Shell_Scripting.pptShell_Scripting.ppt
Shell_Scripting.pptKiranMantri
 
The structure of Linux - Introduction to Linux for bioinformatics
The structure of Linux - Introduction to Linux for bioinformaticsThe structure of Linux - Introduction to Linux for bioinformatics
The structure of Linux - Introduction to Linux for bioinformaticsBITS
 
Module 3 Using Linux Softwares.
Module 3 Using Linux Softwares.Module 3 Using Linux Softwares.
Module 3 Using Linux Softwares.Tushar B Kute
 
OpenGurukul : Operating System : Linux
OpenGurukul : Operating System : LinuxOpenGurukul : Operating System : Linux
OpenGurukul : Operating System : LinuxOpen Gurukul
 
Linux basic for CADD biologist
Linux basic for CADD biologistLinux basic for CADD biologist
Linux basic for CADD biologistAjay Murali
 
Introduction to linux2
Introduction to linux2Introduction to linux2
Introduction to linux2Gourav Varma
 
Nguyễn Vũ Hưng: Basic Linux Power Tools
Nguyễn Vũ Hưng: Basic Linux Power Tools Nguyễn Vũ Hưng: Basic Linux Power Tools
Nguyễn Vũ Hưng: Basic Linux Power Tools Vu Hung Nguyen
 
An Introduction to Linux
An Introduction to LinuxAn Introduction to Linux
An Introduction to LinuxDimas Prasetyo
 
Linux_Ch2 Lecture (1).pdf
Linux_Ch2 Lecture (1).pdfLinux_Ch2 Lecture (1).pdf
Linux_Ch2 Lecture (1).pdfAllinOne746595
 
linux commands.pdf
linux commands.pdflinux commands.pdf
linux commands.pdfamitkamble79
 
Unix primer
Unix primerUnix primer
Unix primerdummy
 
8.1.intro unix
8.1.intro unix8.1.intro unix
8.1.intro unixsouthees
 
Basic shell programs assignment 1_solution_manual
Basic shell programs assignment 1_solution_manualBasic shell programs assignment 1_solution_manual
Basic shell programs assignment 1_solution_manualKuntal Bhowmick
 
Linux Introduction (Commands)
Linux Introduction (Commands)Linux Introduction (Commands)
Linux Introduction (Commands)anandvaidya
 
Linux introduction-commands2338
Linux introduction-commands2338Linux introduction-commands2338
Linux introduction-commands2338Cam YP Co., Ltd
 

Ähnlich wie BITS: Introduction to Linux - Text manipulation tools for bioinformatics (20)

Command Line Tools
Command Line ToolsCommand Line Tools
Command Line Tools
 
Unix Basics For Testers
Unix Basics For TestersUnix Basics For Testers
Unix Basics For Testers
 
Linux shell scripting
Linux shell scriptingLinux shell scripting
Linux shell scripting
 
Shell_Scripting.ppt
Shell_Scripting.pptShell_Scripting.ppt
Shell_Scripting.ppt
 
The structure of Linux - Introduction to Linux for bioinformatics
The structure of Linux - Introduction to Linux for bioinformaticsThe structure of Linux - Introduction to Linux for bioinformatics
The structure of Linux - Introduction to Linux for bioinformatics
 
Module 3 Using Linux Softwares.
Module 3 Using Linux Softwares.Module 3 Using Linux Softwares.
Module 3 Using Linux Softwares.
 
Directories description
Directories descriptionDirectories description
Directories description
 
OpenGurukul : Operating System : Linux
OpenGurukul : Operating System : LinuxOpenGurukul : Operating System : Linux
OpenGurukul : Operating System : Linux
 
Linux basic for CADD biologist
Linux basic for CADD biologistLinux basic for CADD biologist
Linux basic for CADD biologist
 
Introduction to linux2
Introduction to linux2Introduction to linux2
Introduction to linux2
 
File system discovery
File system discovery File system discovery
File system discovery
 
Nguyễn Vũ Hưng: Basic Linux Power Tools
Nguyễn Vũ Hưng: Basic Linux Power Tools Nguyễn Vũ Hưng: Basic Linux Power Tools
Nguyễn Vũ Hưng: Basic Linux Power Tools
 
An Introduction to Linux
An Introduction to LinuxAn Introduction to Linux
An Introduction to Linux
 
Linux_Ch2 Lecture (1).pdf
Linux_Ch2 Lecture (1).pdfLinux_Ch2 Lecture (1).pdf
Linux_Ch2 Lecture (1).pdf
 
linux commands.pdf
linux commands.pdflinux commands.pdf
linux commands.pdf
 
Unix primer
Unix primerUnix primer
Unix primer
 
8.1.intro unix
8.1.intro unix8.1.intro unix
8.1.intro unix
 
Basic shell programs assignment 1_solution_manual
Basic shell programs assignment 1_solution_manualBasic shell programs assignment 1_solution_manual
Basic shell programs assignment 1_solution_manual
 
Linux Introduction (Commands)
Linux Introduction (Commands)Linux Introduction (Commands)
Linux Introduction (Commands)
 
Linux introduction-commands2338
Linux introduction-commands2338Linux introduction-commands2338
Linux introduction-commands2338
 

Mehr von BITS

RNA-seq for DE analysis: detecting differential expression - part 5
RNA-seq for DE analysis: detecting differential expression - part 5RNA-seq for DE analysis: detecting differential expression - part 5
RNA-seq for DE analysis: detecting differential expression - part 5BITS
 
RNA-seq for DE analysis: extracting counts and QC - part 4
RNA-seq for DE analysis: extracting counts and QC - part 4RNA-seq for DE analysis: extracting counts and QC - part 4
RNA-seq for DE analysis: extracting counts and QC - part 4BITS
 
RNA-seq for DE analysis: the biology behind observed changes - part 6
RNA-seq for DE analysis: the biology behind observed changes - part 6RNA-seq for DE analysis: the biology behind observed changes - part 6
RNA-seq for DE analysis: the biology behind observed changes - part 6BITS
 
RNA-seq: analysis of raw data and preprocessing - part 2
RNA-seq: analysis of raw data and preprocessing - part 2RNA-seq: analysis of raw data and preprocessing - part 2
RNA-seq: analysis of raw data and preprocessing - part 2BITS
 
RNA-seq: general concept, goal and experimental design - part 1
RNA-seq: general concept, goal and experimental design - part 1RNA-seq: general concept, goal and experimental design - part 1
RNA-seq: general concept, goal and experimental design - part 1BITS
 
RNA-seq: Mapping and quality control - part 3
RNA-seq: Mapping and quality control - part 3RNA-seq: Mapping and quality control - part 3
RNA-seq: Mapping and quality control - part 3BITS
 
Productivity tips - Introduction to linux for bioinformatics
Productivity tips - Introduction to linux for bioinformaticsProductivity tips - Introduction to linux for bioinformatics
Productivity tips - Introduction to linux for bioinformaticsBITS
 
Text mining on the command line - Introduction to linux for bioinformatics
Text mining on the command line - Introduction to linux for bioinformaticsText mining on the command line - Introduction to linux for bioinformatics
Text mining on the command line - Introduction to linux for bioinformaticsBITS
 
Managing your data - Introduction to Linux for bioinformatics
Managing your data - Introduction to Linux for bioinformaticsManaging your data - Introduction to Linux for bioinformatics
Managing your data - Introduction to Linux for bioinformaticsBITS
 
Introduction to Linux for bioinformatics
Introduction to Linux for bioinformaticsIntroduction to Linux for bioinformatics
Introduction to Linux for bioinformaticsBITS
 
BITS - Genevestigator to easily access transcriptomics data
BITS - Genevestigator to easily access transcriptomics dataBITS - Genevestigator to easily access transcriptomics data
BITS - Genevestigator to easily access transcriptomics dataBITS
 
BITS - Comparative genomics: the Contra tool
BITS - Comparative genomics: the Contra toolBITS - Comparative genomics: the Contra tool
BITS - Comparative genomics: the Contra toolBITS
 
BITS - Comparative genomics on the genome level
BITS - Comparative genomics on the genome levelBITS - Comparative genomics on the genome level
BITS - Comparative genomics on the genome levelBITS
 
BITS - Comparative genomics: gene family analysis
BITS - Comparative genomics: gene family analysisBITS - Comparative genomics: gene family analysis
BITS - Comparative genomics: gene family analysisBITS
 
BITS - Introduction to comparative genomics
BITS - Introduction to comparative genomicsBITS - Introduction to comparative genomics
BITS - Introduction to comparative genomicsBITS
 
BITS - Protein inference from mass spectrometry data
BITS - Protein inference from mass spectrometry dataBITS - Protein inference from mass spectrometry data
BITS - Protein inference from mass spectrometry dataBITS
 
BITS - Overview of sequence databases for mass spectrometry data analysis
BITS - Overview of sequence databases for mass spectrometry data analysisBITS - Overview of sequence databases for mass spectrometry data analysis
BITS - Overview of sequence databases for mass spectrometry data analysisBITS
 
BITS - Search engines for mass spec data
BITS - Search engines for mass spec dataBITS - Search engines for mass spec data
BITS - Search engines for mass spec dataBITS
 
BITS - Introduction to proteomics
BITS - Introduction to proteomicsBITS - Introduction to proteomics
BITS - Introduction to proteomicsBITS
 
BITS - Introduction to Mass Spec data generation
BITS - Introduction to Mass Spec data generationBITS - Introduction to Mass Spec data generation
BITS - Introduction to Mass Spec data generationBITS
 

Mehr von BITS (20)

RNA-seq for DE analysis: detecting differential expression - part 5
RNA-seq for DE analysis: detecting differential expression - part 5RNA-seq for DE analysis: detecting differential expression - part 5
RNA-seq for DE analysis: detecting differential expression - part 5
 
RNA-seq for DE analysis: extracting counts and QC - part 4
RNA-seq for DE analysis: extracting counts and QC - part 4RNA-seq for DE analysis: extracting counts and QC - part 4
RNA-seq for DE analysis: extracting counts and QC - part 4
 
RNA-seq for DE analysis: the biology behind observed changes - part 6
RNA-seq for DE analysis: the biology behind observed changes - part 6RNA-seq for DE analysis: the biology behind observed changes - part 6
RNA-seq for DE analysis: the biology behind observed changes - part 6
 
RNA-seq: analysis of raw data and preprocessing - part 2
RNA-seq: analysis of raw data and preprocessing - part 2RNA-seq: analysis of raw data and preprocessing - part 2
RNA-seq: analysis of raw data and preprocessing - part 2
 
RNA-seq: general concept, goal and experimental design - part 1
RNA-seq: general concept, goal and experimental design - part 1RNA-seq: general concept, goal and experimental design - part 1
RNA-seq: general concept, goal and experimental design - part 1
 
RNA-seq: Mapping and quality control - part 3
RNA-seq: Mapping and quality control - part 3RNA-seq: Mapping and quality control - part 3
RNA-seq: Mapping and quality control - part 3
 
Productivity tips - Introduction to linux for bioinformatics
Productivity tips - Introduction to linux for bioinformaticsProductivity tips - Introduction to linux for bioinformatics
Productivity tips - Introduction to linux for bioinformatics
 
Text mining on the command line - Introduction to linux for bioinformatics
Text mining on the command line - Introduction to linux for bioinformaticsText mining on the command line - Introduction to linux for bioinformatics
Text mining on the command line - Introduction to linux for bioinformatics
 
Managing your data - Introduction to Linux for bioinformatics
Managing your data - Introduction to Linux for bioinformaticsManaging your data - Introduction to Linux for bioinformatics
Managing your data - Introduction to Linux for bioinformatics
 
Introduction to Linux for bioinformatics
Introduction to Linux for bioinformaticsIntroduction to Linux for bioinformatics
Introduction to Linux for bioinformatics
 
BITS - Genevestigator to easily access transcriptomics data
BITS - Genevestigator to easily access transcriptomics dataBITS - Genevestigator to easily access transcriptomics data
BITS - Genevestigator to easily access transcriptomics data
 
BITS - Comparative genomics: the Contra tool
BITS - Comparative genomics: the Contra toolBITS - Comparative genomics: the Contra tool
BITS - Comparative genomics: the Contra tool
 
BITS - Comparative genomics on the genome level
BITS - Comparative genomics on the genome levelBITS - Comparative genomics on the genome level
BITS - Comparative genomics on the genome level
 
BITS - Comparative genomics: gene family analysis
BITS - Comparative genomics: gene family analysisBITS - Comparative genomics: gene family analysis
BITS - Comparative genomics: gene family analysis
 
BITS - Introduction to comparative genomics
BITS - Introduction to comparative genomicsBITS - Introduction to comparative genomics
BITS - Introduction to comparative genomics
 
BITS - Protein inference from mass spectrometry data
BITS - Protein inference from mass spectrometry dataBITS - Protein inference from mass spectrometry data
BITS - Protein inference from mass spectrometry data
 
BITS - Overview of sequence databases for mass spectrometry data analysis
BITS - Overview of sequence databases for mass spectrometry data analysisBITS - Overview of sequence databases for mass spectrometry data analysis
BITS - Overview of sequence databases for mass spectrometry data analysis
 
BITS - Search engines for mass spec data
BITS - Search engines for mass spec dataBITS - Search engines for mass spec data
BITS - Search engines for mass spec data
 
BITS - Introduction to proteomics
BITS - Introduction to proteomicsBITS - Introduction to proteomics
BITS - Introduction to proteomics
 
BITS - Introduction to Mass Spec data generation
BITS - Introduction to Mass Spec data generationBITS - Introduction to Mass Spec data generation
BITS - Introduction to Mass Spec data generation
 

Kürzlich hochgeladen

BASLIQ CURRENT LOOKBOOK LOOKBOOK(1) (1).pdf
BASLIQ CURRENT LOOKBOOK LOOKBOOK(1) (1).pdfBASLIQ CURRENT LOOKBOOK LOOKBOOK(1) (1).pdf
BASLIQ CURRENT LOOKBOOK LOOKBOOK(1) (1).pdfSoniaTolstoy
 
Paris 2024 Olympic Geographies - an activity
Paris 2024 Olympic Geographies - an activityParis 2024 Olympic Geographies - an activity
Paris 2024 Olympic Geographies - an activityGeoBlogs
 
How to Make a Pirate ship Primary Education.pptx
How to Make a Pirate ship Primary Education.pptxHow to Make a Pirate ship Primary Education.pptx
How to Make a Pirate ship Primary Education.pptxmanuelaromero2013
 
Activity 01 - Artificial Culture (1).pdf
Activity 01 - Artificial Culture (1).pdfActivity 01 - Artificial Culture (1).pdf
Activity 01 - Artificial Culture (1).pdfciinovamais
 
Presentation by Andreas Schleicher Tackling the School Absenteeism Crisis 30 ...
Presentation by Andreas Schleicher Tackling the School Absenteeism Crisis 30 ...Presentation by Andreas Schleicher Tackling the School Absenteeism Crisis 30 ...
Presentation by Andreas Schleicher Tackling the School Absenteeism Crisis 30 ...EduSkills OECD
 
Organic Name Reactions for the students and aspirants of Chemistry12th.pptx
Organic Name Reactions for the students and aspirants of Chemistry12th.pptxOrganic Name Reactions for the students and aspirants of Chemistry12th.pptx
Organic Name Reactions for the students and aspirants of Chemistry12th.pptxVS Mahajan Coaching Centre
 
Industrial Policy - 1948, 1956, 1973, 1977, 1980, 1991
Industrial Policy - 1948, 1956, 1973, 1977, 1980, 1991Industrial Policy - 1948, 1956, 1973, 1977, 1980, 1991
Industrial Policy - 1948, 1956, 1973, 1977, 1980, 1991RKavithamani
 
“Oh GOSH! Reflecting on Hackteria's Collaborative Practices in a Global Do-It...
“Oh GOSH! Reflecting on Hackteria's Collaborative Practices in a Global Do-It...“Oh GOSH! Reflecting on Hackteria's Collaborative Practices in a Global Do-It...
“Oh GOSH! Reflecting on Hackteria's Collaborative Practices in a Global Do-It...Marc Dusseiller Dusjagr
 
Accessible design: Minimum effort, maximum impact
Accessible design: Minimum effort, maximum impactAccessible design: Minimum effort, maximum impact
Accessible design: Minimum effort, maximum impactdawncurless
 
Introduction to ArtificiaI Intelligence in Higher Education
Introduction to ArtificiaI Intelligence in Higher EducationIntroduction to ArtificiaI Intelligence in Higher Education
Introduction to ArtificiaI Intelligence in Higher Educationpboyjonauth
 
Z Score,T Score, Percential Rank and Box Plot Graph
Z Score,T Score, Percential Rank and Box Plot GraphZ Score,T Score, Percential Rank and Box Plot Graph
Z Score,T Score, Percential Rank and Box Plot GraphThiyagu K
 
Separation of Lanthanides/ Lanthanides and Actinides
Separation of Lanthanides/ Lanthanides and ActinidesSeparation of Lanthanides/ Lanthanides and Actinides
Separation of Lanthanides/ Lanthanides and ActinidesFatimaKhan178732
 
mini mental status format.docx
mini mental status format.docxmini mental status format.docx
mini mental status format.docxPoojaSen20
 
Arihant handbook biology for class 11 .pdf
Arihant handbook biology for class 11 .pdfArihant handbook biology for class 11 .pdf
Arihant handbook biology for class 11 .pdfchloefrazer622
 
POINT- BIOCHEMISTRY SEM 2 ENZYMES UNIT 5.pptx
POINT- BIOCHEMISTRY SEM 2 ENZYMES UNIT 5.pptxPOINT- BIOCHEMISTRY SEM 2 ENZYMES UNIT 5.pptx
POINT- BIOCHEMISTRY SEM 2 ENZYMES UNIT 5.pptxSayali Powar
 
18-04-UA_REPORT_MEDIALITERAСY_INDEX-DM_23-1-final-eng.pdf
18-04-UA_REPORT_MEDIALITERAСY_INDEX-DM_23-1-final-eng.pdf18-04-UA_REPORT_MEDIALITERAСY_INDEX-DM_23-1-final-eng.pdf
18-04-UA_REPORT_MEDIALITERAСY_INDEX-DM_23-1-final-eng.pdfssuser54595a
 
Advanced Views - Calendar View in Odoo 17
Advanced Views - Calendar View in Odoo 17Advanced Views - Calendar View in Odoo 17
Advanced Views - Calendar View in Odoo 17Celine George
 

Kürzlich hochgeladen (20)

BASLIQ CURRENT LOOKBOOK LOOKBOOK(1) (1).pdf
BASLIQ CURRENT LOOKBOOK LOOKBOOK(1) (1).pdfBASLIQ CURRENT LOOKBOOK LOOKBOOK(1) (1).pdf
BASLIQ CURRENT LOOKBOOK LOOKBOOK(1) (1).pdf
 
Paris 2024 Olympic Geographies - an activity
Paris 2024 Olympic Geographies - an activityParis 2024 Olympic Geographies - an activity
Paris 2024 Olympic Geographies - an activity
 
How to Make a Pirate ship Primary Education.pptx
How to Make a Pirate ship Primary Education.pptxHow to Make a Pirate ship Primary Education.pptx
How to Make a Pirate ship Primary Education.pptx
 
Activity 01 - Artificial Culture (1).pdf
Activity 01 - Artificial Culture (1).pdfActivity 01 - Artificial Culture (1).pdf
Activity 01 - Artificial Culture (1).pdf
 
Presentation by Andreas Schleicher Tackling the School Absenteeism Crisis 30 ...
Presentation by Andreas Schleicher Tackling the School Absenteeism Crisis 30 ...Presentation by Andreas Schleicher Tackling the School Absenteeism Crisis 30 ...
Presentation by Andreas Schleicher Tackling the School Absenteeism Crisis 30 ...
 
Organic Name Reactions for the students and aspirants of Chemistry12th.pptx
Organic Name Reactions for the students and aspirants of Chemistry12th.pptxOrganic Name Reactions for the students and aspirants of Chemistry12th.pptx
Organic Name Reactions for the students and aspirants of Chemistry12th.pptx
 
Industrial Policy - 1948, 1956, 1973, 1977, 1980, 1991
Industrial Policy - 1948, 1956, 1973, 1977, 1980, 1991Industrial Policy - 1948, 1956, 1973, 1977, 1980, 1991
Industrial Policy - 1948, 1956, 1973, 1977, 1980, 1991
 
“Oh GOSH! Reflecting on Hackteria's Collaborative Practices in a Global Do-It...
“Oh GOSH! Reflecting on Hackteria's Collaborative Practices in a Global Do-It...“Oh GOSH! Reflecting on Hackteria's Collaborative Practices in a Global Do-It...
“Oh GOSH! Reflecting on Hackteria's Collaborative Practices in a Global Do-It...
 
Accessible design: Minimum effort, maximum impact
Accessible design: Minimum effort, maximum impactAccessible design: Minimum effort, maximum impact
Accessible design: Minimum effort, maximum impact
 
Introduction to ArtificiaI Intelligence in Higher Education
Introduction to ArtificiaI Intelligence in Higher EducationIntroduction to ArtificiaI Intelligence in Higher Education
Introduction to ArtificiaI Intelligence in Higher Education
 
Z Score,T Score, Percential Rank and Box Plot Graph
Z Score,T Score, Percential Rank and Box Plot GraphZ Score,T Score, Percential Rank and Box Plot Graph
Z Score,T Score, Percential Rank and Box Plot Graph
 
TataKelola dan KamSiber Kecerdasan Buatan v022.pdf
TataKelola dan KamSiber Kecerdasan Buatan v022.pdfTataKelola dan KamSiber Kecerdasan Buatan v022.pdf
TataKelola dan KamSiber Kecerdasan Buatan v022.pdf
 
Separation of Lanthanides/ Lanthanides and Actinides
Separation of Lanthanides/ Lanthanides and ActinidesSeparation of Lanthanides/ Lanthanides and Actinides
Separation of Lanthanides/ Lanthanides and Actinides
 
Mattingly "AI & Prompt Design: The Basics of Prompt Design"
Mattingly "AI & Prompt Design: The Basics of Prompt Design"Mattingly "AI & Prompt Design: The Basics of Prompt Design"
Mattingly "AI & Prompt Design: The Basics of Prompt Design"
 
mini mental status format.docx
mini mental status format.docxmini mental status format.docx
mini mental status format.docx
 
Arihant handbook biology for class 11 .pdf
Arihant handbook biology for class 11 .pdfArihant handbook biology for class 11 .pdf
Arihant handbook biology for class 11 .pdf
 
Staff of Color (SOC) Retention Efforts DDSD
Staff of Color (SOC) Retention Efforts DDSDStaff of Color (SOC) Retention Efforts DDSD
Staff of Color (SOC) Retention Efforts DDSD
 
POINT- BIOCHEMISTRY SEM 2 ENZYMES UNIT 5.pptx
POINT- BIOCHEMISTRY SEM 2 ENZYMES UNIT 5.pptxPOINT- BIOCHEMISTRY SEM 2 ENZYMES UNIT 5.pptx
POINT- BIOCHEMISTRY SEM 2 ENZYMES UNIT 5.pptx
 
18-04-UA_REPORT_MEDIALITERAСY_INDEX-DM_23-1-final-eng.pdf
18-04-UA_REPORT_MEDIALITERAСY_INDEX-DM_23-1-final-eng.pdf18-04-UA_REPORT_MEDIALITERAСY_INDEX-DM_23-1-final-eng.pdf
18-04-UA_REPORT_MEDIALITERAСY_INDEX-DM_23-1-final-eng.pdf
 
Advanced Views - Calendar View in Odoo 17
Advanced Views - Calendar View in Odoo 17Advanced Views - Calendar View in Odoo 17
Advanced Views - Calendar View in Odoo 17
 

BITS: Introduction to Linux - Text manipulation tools for bioinformatics

  • 1.
  • 2.
  • 3.
  • 4.
  • 5. And there we are... username Machine name location
  • 6.
  • 7. The File System Tree / bin boot dev etc home media root sbin tmp usr var james bin sbin share bin sbin share local lib log mail run spool tmp Aka ~ (for james) The variable PATH contains the paths of the bin folders. See command env.
  • 8.
  • 9.
  • 10.
  • 11.
  • 12.
  • 13.
  • 14.
  • 15.
  • 16.
  • 17.
  • 18.
  • 19.
  • 20.
  • 21.
  • 22.
  • 23.
  • 24.
  • 25.
  • 26.
  • 27.
  • 28.
  • 29.
  • 30.
  • 31.
  • 32.
  • 33.
  • 34.
  • 40.
  • 41.
  • 42.
  • 43.
  • 44.
  • 45.
  • 46.
  • 47.
  • 48.
  • 49.
  • 50.
  • 51.
  • 52.
  • 53.
  • 54.
  • 55.
  • 56.
  • 57.
  • 58.
  • 59.
  • 60.
  • 61.
  • 62.
  • 63.
  • 64.
  • 65.
  • 66.
  • 67.
  • 68.
  • 69.
  • 70.
  • 71.
  • 72.
  • 73.
  • 74.
  • 75.
  • 76.
  • 77.
  • 78.
  • 79.
  • 80. Comparing files – GUI (meld)
  • 81.
  • 82.
  • 83.
  • 84.
  • 85.