Quick Start AutoCSA Guide

1. Introduction
2. Installing Java
3. Download AutoCSA and the Example Set
4. Install AutoCSA
5. Setting Up AutoCSA
6. Running AutoCSA

1. Introduction

This document will guide you through setting up AutoCSA to run with the example set provided on the website. The example set contains 4 mutations, a heterozygous substitution, a homozygous substitution, a heterozygous indel and a homozygous indel. This guide's aim is to get AutoCSA running as quickly as possible on your system, if more information is required please consult the Installation and User Guide.

2. Installing Java

If you already have a version of java running on your machine this stage can be skipped. Otherwise you will need to install an up to date version of the Java Virtual Machine (JVM). The JVM is available from the Sun Microsystems website (http://www.java.com).

Download java software from (http://www.java.com). Just click the download button on the java.com website and the webpages will guide you through the installation process and will also test if the install has been successful (Figure 1).

Figure 1 java.com website

3. Download AutoCSA and the Example Set

AutoCSA and an example dataset are available from here. You just need to click on the link and save the file to a folder on your computer. Once downloaded the zip file must be uncompressed, for PC users right click on the zip file and select extract all, which will run the Extraction Wizard program. This should result in a directory called AutoCSA being created containing the following:

Figure 2 Example_data Subfolders

4. Install AutoCSA

AutoCSA comes with an installer so you just need to double click on csa-installer.jar which was included in the root directory of the zip download. The installer will then guide you through the initial setup stages.

Click through the installation guide. You must accept our license agreement in order to complete the installation. The guide will also prompt you for where you would like the software installed. The default location is C:\Program Files\AutoCSA (hint:- it is worth noting where the software is installed as you will need to go to this folder to run AutoCSA). Once this has been completed the installation guide will automatically run the setup wizard (see next section).

5. Setting up AutoCSA

The initial setup of AutoCSA has been simplified by the use of a setup wizard which will guide you through a series of menus and questions. The wizard system prompts the user for where the trace files are located, where the output should go and the make up of the trace file name.

5a) Defining Input/Ouput Folders and Filename Format

The second page of the wizard prompts you for an example of a sample trace file and 2 folder locations (folders for input/output, Figure 3). The following three bullet points should help you to fill in this page of the wizard:-

Figure 3 Page 2 of the Setup Wizard

The wizard then takes the sample file that you provided on the last page and using the file as an example asks a series of questions so the fields in the filename can be defined. Below are the questions that you will be asked and in red is what should be entered at each stage (Figure 4).

Figure 4 Completed Page 3 of the Setup Wizard

5b) DNA Amplimer Sequence and the Amplimer.Properties File

Once the fields for the trace file have been defined the wizard then goes onto defining the DNA amplimer sequences. In order for AutoCSA to run it must have the actual DNA sequence of the amplimer. A data file containing the amplimer information for the example set has been provided in the zip file called amplimer.properties. This means this stage can be skipped by clicking the finish button (Figure 5). However, in order to run AutoCSA the amplimer.properties file must be copied to the standaloneCSA directory from the example_set directory (Figure 6).

Figure 5 Page to add Amplimer Sequence can be skipped

Before going onto the next section you must copy the amplimer.properties file from the example_set folder to the standaloneCSA directory or AutoCSA will not run properly (Figure 6).

Figure 6 Copy the Amplimer.properties file to the StandaloneCSA folder

6. Running AutoCSA

Once setup is complete AutoCSA can be run by clicking on the run icon in the folder where AutoCSA was installed (Figure 7). The default location is C:\Program Files\AutoCSA. You must make sure that the new amplimer.properties file has been copied from the example_set directory to this directory or AutoCSA will not run properly.

Figure 7 StandaloneCSA folder, to run AutoCSA double click the run icon

A terminal will appear which will display the progress of the software and also any errors (Figure 8). Once AutoCSA has finished running it will automatically open a web browser with a summary of the results. For further information please consult the Installation and User Guide.

Figure 8 Terminal Displaying Progress of AutoCSA