Exploring gene annotations on the command-line

Author: Gavin Band

Welcome! In this tutorial we will show how to use the UNIX command line to explore the human gene annotations. This tutorial has two main objectives:

• To demonstrate some useful ways of working in the UNIX command line;
• And to get you to start understanding gene annotation data - that is, the core data files which represent our knowledge of human genes.

The information in these files includes such things as where genes are in the genome, how they are transcribed, which bits gets turned into proteins and so on. They are pretty important files!

This is not a full tutorial on command-line processing, but here is a table of some of the UNIX commands we'll use. If you're not familiar with these, don't worry: there are a lot of commands and it takes a while to learn them. Try the example commands now in your terminal:

Command	What it does	Example
ls	Lists files in a directory	ls
mkdir	Make a new directory	mkdir genes_tutorial
cd	Changes the current directory	cd genes_tutorial
echo	Print some text (that can be redirected to a file.)	echo "Hello all\ngenes" > file.txt
cat	Print the output of one or more files.	cat file.txt
less	Interactively explore a file (press q to quit)	less file.txt
cut	Extract specific columns from a file	cut -d' ' -f1 file.txt
grep	Search for a string (or regular expression)	grep "Hello" file.txt
awk	General-purpose tool. (We'll use to select lines with specific values in a column.)	awk '$1 == "Hello"' file.txt
sort	Sort rows alphabetically	sort file.txt
uniq	Gather and count unique values	uniq -c file.txt
gzip/gunzip	General-purpose compression/decompression.	gzip file.txt

Here are some tips that will make life easier:

Tips and tricks

• The command line will auto-complete filenames for you if you press the tab key - this saves a lot of typing.
• Press the up arrow to go back in your command history - you can then edit/rerun the same command.
• In filenames, ./ indicates the current directory, while ../ indicates the parent directory (i.e. one higher up.) so for example cd ../ takes you one level higher.

ls is particularly useful for looking around - for example

• ls on its own prints a simple listing.
• ls -a will also include hidden files - these are filenames starting with a . that are usually excluded.
• ls -l will print a long listing - dates, file owners, file sizes, etc. (A command I use a lot is ls -lht which lists files ordered by modification time with human-readable file sizes.)

When you're ready, move on to download the tutorial data.