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Unix Tutorial Practice
Jeanie Lim edited this page Sep 11, 2016
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Command | Description |
---|---|
echo $HOME |
|
ls |
list files and directories |
ls -a |
list all files and directories |
mkdir |
make a directory |
cd
|
change to named directory |
cd |
change to home-directory |
cd ~ |
change to home-directory |
cd .. |
change to parent directory |
pwd |
display the path of the current directory |
Command | Description |
---|---|
cp file1 file2 |
copy file1 and call it file2 |
mv file1 file2 |
move or rename file1 to file2 |
rm file |
remove a file |
rmdir <directory> |
remove a directory |
Command | Description |
---|---|
cat file |
display a file |
less file |
display a file a page at a time |
head file |
display the first few lines of a file |
tail file |
display the last few lines of a file |
grep _'keyword'_ file |
search a file for keywords |
wc <file> |
count number of lines/words/characters in file |
Command | Description |
---|---|
command > file |
redirect standard output to a file |
command >> file |
append standard output to a file |
command < file |
redirect standard input from a file |
`command1 | command2` |
cat file1 file2 > file0 |
concatenate file1 and file2 to file0 |
sort |
sort data |
who |
list users currently logged in |
6-iii. Integrated assignment answers
#Table of Contents
- Module 0 Setting Up for Data Analysis
- Introduction to High Performance Computing Cluster
- Connecting to MGHPCC
- Computing Environment
- Unix Tutorial Part 1: UNIX Bootcamp
- Unix Tutorial Part 2: Shell Scripting
- Unix Tutorial Practice
- Submitting computing jobs to HPC using LSF
- Ignore: Git Tutorial
- Module 1 Introduction/ Overview
- Overview of RNA-seq Experiment
- RNA-Seq Analysis Pipeline
- RNA-Seq Input Data
- RNA-seq File Formats and Software-Specific Files
- Getting Data for Analysis
- Module 2 Quality Control
- Module 3 Tuxedo Pipeline
- The Tuxedo Pipeline
- Read Alignment with TopHat2
- Transcript Assembly with Cufflinks
- Differential Analysis with Cuffdiff
- Visualization with CummeRbund
- Resources and Reference