RNA-seq course basic linux commands

pwd

tells you where you are

ls

list the content of the current directory

ls <directory name>

list the content of a directory

cd <directory name>

go to the specified directory

cd ~ (or cd)

go to your home directory

cd ..

go to the parent directory

tree <directory name>

list the content of a directory in a tree-like format

mkdir <directory name>

creates specified directory

less, more

view text with paging

head

prints first lines of a file

tail

prints last lines of a file

cat

print content of a file into the screen

zcat

print content of a gzip compressed file

rm <file name>

remove file

cp <file1> <file2>

copy file1 into file2

mv <file1> <file2>

rename file1 to file2

gedit <file>

text editor with graphical user interface

vi <file>

text editor with command mode interface (See a-beginners-guide-to-editing-text-files-with-vi)

emacs <file>

text editor with graphical user interface

grep <pattern>

show lines of text containing a given pattern

grep -v <pattern>

show lines of text not containing a given pattern

sort

sort linesof text files

wc

counting words, lines and characters

> (output redirection)

allows to redirect the output to a file

| (pipe)

allows to send output from one program to another

cut

to extract portion of a file by selecting columns

echo

input a line of text and display it on standard output

awk '/www/ { print $0 }' <file>

search for the pattern 'www' in the each line of the file

awk '$3=="www"' <file>

search for pattern 'www' in the third column of the file

awk 'length($0) > 80' <file>

print every line in the file that is longer than 80 characters

awk 'NR % 2 == 0' <file>

print even-numbered lines in the file