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Next Generation Sequence Analysis

A project by Dr. David Coil, the Comai Lab, and the UCD Genome Center

Around 2007, the advent of next generation sequencing (= a lot of DNA sequence for much less $) opened a new approach to biology. The sheer volume of DNA data produced by this method appears daunting. It does not need to be so. A little bit of knowledge of specialized computer techniques can lead us a long way. This page links to a number of our tutorial videos, some ready, some under production, on simple methods for next-generation sequence analysis.

These videos are aimed primarily at biologists who lack the bioinformatics knowledge to analyze these large data sets. Therefore biological background knowledge is assumed.

Using the Terminal (4 videos)

This series of videos looks at using the Terminal program (which comes on every Macintosh computer) to view and parse large sequence datasets.

NOTE FOR PC USERS: All Macs are Unix-based machines and the Terminal is simply a command line prompt that allows the user to work in Unix. There is no default equivalent found within Windows. However, it is possible to install a Unix environment on a Windows machine. In this case, these videos will still be of assistance, but some minor details (such as the display of outputs) will differ from what you will see here). For instructions on installing a Unix environment in Windows see this article.


Video 1 - Using the Terminal: "grep" and "less"

This video will introduce the Terminal program and discuss two basic commands. The first is "less" which is used to display data, the second is "grep" which is used to search or count within the data.

http://www.youtube.com/user/Arturgreensward?feature=mhum#p/a/u/0/zRZT4nQP3sE

Video 2 - A Sample Experimental Design

This video briefly discusses the biological background of the experimental data set used in the next two videos.

Video 3 - Using the Terminal: Viewing and Parsing Data

This video takes a look at the data from an actual experiment where an Illumina sequencing run was aligned to a cDNA database. Here the user will learn how to navigate through the output and how to parse the data file using the "grep" command.


Video 4 - Using the Terminal: A Sample Data Analysis

This video shows how to perform a basic data analysis on the same dataset as above. Here we undertake an "in-silico Northern" analysis and look at gene expression differences for a target gene as well as a housekeeping gene.


Locating and Analyzing Public Datasets with Free Tools

This series of videos is currently under development.

The goal of this video series is for a researcher to be able to perform useful and complex bioinformatic analyses of next-generation sequencing data without ever leaving the desk, purchasing any software, or hiring a bioinformatician.

Here we will start by locating publicly available datasets generated by next-generation sequencing techniques. We will learn how to perform an alignment of a sequencing dataset to a cDNA or genomic database, and then how to perform a complete analysis of the resulting alignment.

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