Introduction to Terminal¶

Overview of Linux¶

Linux is a free OS and very similiar to the UNIX OS in terms of concepts and features.

Linux System Structure¶

Linux system has three main components:

Kernel:

It controls system hardware including memory, processors, disks, and I/ O (Input/ Output) devices. It schedules processes, enforces security, manages user access, and so on. The kernel receives instructions from the shell, engages appropriate hardware resources, and acts as instructed.

Shell:

(This the important part for our class) The shell is a program that accepts and interprets text-mode commands. The user provides instructions (commands) to the shell, which are interpreted and passed to the kernel for processing.

Hierarchical directory structure:

Linux uses the conventional hierarchical directory structure where directories may contain both files and sub-directories. Sub-directories may further hold more files and sub-directories. A subdirectory, also referred to as a child directory, is a directory located under a parent directory. >

/home/ username/dir1/ subdir1 -root (parent of home)
home - sub-directory or child of / (root)

Starting a Shell¶

Through SSH
Using graphical interface

[] prompt, waiting for you to start entering commands.

Terminal Commands¶

pwd (Print Working Directory)¶

When you first login, you are logged into your home directory (/home/username).

To find out what is your current working directory, type

$ pwd
/home/kiriya

mkdir (makding a directory)¶

To make a subdirectory called Software in your home directory, type

$ mkdir Software

ls (list)¶

To see what is inside the home directory, type

$ ls

cd (change directory)¶

To change the current directory to the “Software”, type

$ cd Software

:~$ cd ../ -by typying this you can go back to where you started.

Excercise¶

Use the Terminal commands we already learned to do the following steps.

Creat following directory structure in your “Home Directory”

RNA-Seq/Reference/Genome

RNA-Seq/Reference/Annotation

RNA-Seq/RAW_Data

RNA-Seq/Adapters

RNA-Seq/QC/Fastqc_Out

RNA-Seq/QC/Adapter_Removed

RNA-Seq/QC/Trimmed

RNA-Seq/Alignment/Tophat2

Note

You might have to use “-p” option to create non-exsisting intermediate directories**

Final output:

File Handling Through the Terminal¶

Displaying Content of a Compressed gunzip File¶

zcat [filename.gz]

$ zcat sequence.fastq.gz | less

De-compressing gunzip File¶

gzip -d [filename.gz]

$ gzip -d sequence.fastq.gz

Displaying Content of a File¶

cat:	display whole content of a file on the screen
less:	display contents of a file onto the screen a page at a time
head:	display first ten lines of a file to the screen
tail:	display last ten lines of a file to the screen

cat [filename]¶

$ cat sequence.fastq | less

less [filename]¶

$ less sequence.fastq

head [filename]¶

$ head sequence.fastq

tail [filename]¶

$ tail sequence.fastq

Renaming a File¶

mv [orginalfile.txt] [newnamefile.txt]

$ mv sequence.fastq new_sequence.fastq

Searching the Contents of a File¶

grep [options] [word_to_find] [filename]

$ grep "@" sequence.fastq
  @D00109:408:C77LEANXX:2:1101:1715:1962 1:N:0:18

Concatenating two or more files¶

cat [fist_file.txt] [second_file.txt] [thrid_file.txt] .... [N_file.txt] > [output_file.txt]

$ cat first.txt second.txt > third.txt

Finally, Compress that File!!¶

gzip [filetocompress]

$ gzip sequence.fastq

Excercise¶

Count the number of sequnces in a fastq.gz file

Note

Use zcat and pip (“|”) the output to grep -c [word_to_grep]