1. Server Connection
a. If you are using a windows machine and the SSH client application, start the SSH Client, by clicking this icon in the desktop 
b. Use the given IP address for the Host name. Use the username and password provided to you, along with the Hostname, to connect to the class server.
c. Your connection window would look like below or similar;
d. Use the ssh command, specifying the username and the ip address, like below, to login in to the server using the mac terminal;.
2. The first 5 commands - pwd,ls,mkdir,cp,cd
a. pwd - Print the path of the current working directory
pwd
b. ls - List items in the current working directory
ls
c. mkdir - Make/create a new directory
mkdir mydemo
d. cp - Copy files(s)/folder(s) from one place to another
cp ~/Desktop/unix/FoxA1_peaks.narrowPeak mydemo
e. cd - Change to a different directory
cd mydemo ls -l ls -a ls -lh
3. The next 5 - mv,head,tail,man,rm
a. Make a copy of the original file
cp FoxA1_peaks.narrowPeak towork.txt
b. mv - Move/Rename file/folder
mv towork.txt peaks.txt ls -lh
c. head - Show the first few /head contents of a file
head peaks.txt head -n 2 peaks.txt head -n 10 peaks.txt > peaks10.txt
d. tail - Show the last few /tail contents of a file
tail peaks.txt tail -n 2 peaks.txt
e. man - Show the manual page for a command
man head
f. rm - Remove a file/folder
ls -l rm peaks10.txt ls -l
4. Useful others - more,less,grep,wc,cat
a. more - Displays the first few lines of a file and lets you scroll through
more peaks.txt
b. less - Like more, but forward and backward
less peaks.txt
c. grep - The powerful search command
grep chr1 peaks.txt > chr1.txt ls -l head chr1.txt tail chr1.txt grep -w chr1 peaks.txt > chr1correct.txt #use word boundary ls -l head chr1correct.txt tail chr1correct.txt rm chr1.txt mv chr1correct.txt chr1.txt ls -l
d. wc - Counts things - letters, words, lines etc.
wc peaks.txt wc -l peaks.txt wc -l chr.txt
e.cat - Concatenate file contents
grep -w chr2 peaks.txt > chr2.txt ls -lh cat chr1.txt cat chr1.txt chr2.txt > chr1and2.txt head chr1and2.txt tail chr1and2.txt wc -l chr1and2.txt
5. Editor
a. nano or vi or vim or emacs
nano f1.txt
b. Enter some text and Ctrl X, to save.
cat f1.txt
c. vi - Visual text editor
vi f2.txt
Press the ‘i’ key, enter some text
Press the ‘esc’ key to get out of the insert modePress :wq to write (save) and quit
cat f2.txt ls -lh
6. Input and Output
6.1. STDIN,STDOUT (>,<)
head -n 2 peaks.txt > first2 ls -lh cat first2 tail -n 2 peaks.txt > last2 cat last2 wc -l < peaks.txt wc -l < last2
6.2. APPEND
The double greater than symbol appends/adds content to the end of a file
cat last2 >> first2 cat first2
6.3. PIPES
Pipes help pass the input/output between one command/program to another command/program
grep -w chr3 peaks.txt | wc -l<br>ls -l | grep chr | wc -l
7. Getting External Data
a. wget - Get data from only URL, from command line
wget hgdownload.cse.ucsc.edu/goldenPath/hg38/database/ncbiRefSeq.txt.gz ls -l gunzip ncbiRefSeq.txt.gz ls -l head ncbiRefSeq.txt