Genomic Analysis at the Unix Command Line

QB3 - Computational Genomics Resource Laboratory

Spring 2012 - Workshop 01

Monday, Feb 13, 2012

Chris Ellison & Aaron Hardin

This workshop will have two sessions: a morning session from 10.00am - 12.30pm and an afternoon session from 1.30pm to 4.00pm. The goal of the workshop is to introduce a naive user to the command line tools available on Unix operating system to facilitate the analysis of Next-Generation Sequence data.

Target audience for this workshop includes scientists hoping to analyze genomic datasets, but have little or no experience with the Unix computing environment or common genomic analysis tools. 

NOTE: This module requires that you use a recent MacOS or Linux based system, so bring a laptop with one of these systems available. 

What are you going to learn? After the morning session, you will be able to navigate the UNIX environment, allowing you to create, manipulate, and store large data files efficiently. You will find that in many ways, the UNIX environment is designed for speed and simplicity in using large files in a way that is unavailable in more "user-friendly" environments like Microsoft Windows or Mac OS. We will conclude the morning session with a set of exercises that demonstrate the power of the UNIX environment to generate a basic description of the Saccharomyces cerevisiae genome. In this afternoon's session, we will extend the morning's lessons to cover a common utility used in high-throughput sequencing, the Bowtie short-read aligner. After the afternoon session, you should be able to generate proper output with the Bowtie aligner, and generate a description similar to the one we'll see in this morning's exercise. 

What are you not going to learn? This module is intended to teach very basic skills for the UNIX environment, allowing students to pursue more instruction with other modules that will guide you through the complications and considerations for proper genomic analysis. Accordingly, we will demonstrate the very basics of using one genomic utility (Bowtie), but we will not venture into the algorithms, the considerations, or the statistics behind a proper analysis. We hope that you are interested enough after finishing this module to pursue those questions with our other instructors.

Requirements:

1. You must be affiliated with a UC Berkeley campus research group

2. Bring a laptop with a recent version of Linux or Mac OS

3. To maximize the benefit of the workshop, preference will be given to those who have not taken this workshop before. People from different research groups will be given priority over multiple attendees from the same group.