Quick Start AutoCSA Guide
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).
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:
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
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:-
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).
The questions are:-
1. Please enter the trace file extension used, e.g. ab1, scf (do not include "."). scf
2. Please enter the character used to divide the components of the file names, e.g. "_". _
3. Please enter the number (shown in the file components table) for the "amplimer name". 1
4. Please enter the number (shown in the file components table) for the "sample name". 2
5. Please enter the number (shown in the file components table) indicating if the trace is a "reference" or a "sample to be screened". 3
6. Please enter the text that defines the reference trace, e.g. "reference". reference
7. Please enter the number (shown in the file components table) indicating if the trace is forward or reverse. 4
8. Please enter the text that defines the forward trace, e.g. "f" or "s", (any numeric characters will be removed). f
9. Please enter the text that defines the reverse trace, e.g. "r" or "a", (any numeric characters will be removed). r
10. Please enter the number (shown in the file components table) indicating which traces are paired together in this experiment, e.g. "Run1", (any non-numeric characters will be removed). 5
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).
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).
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
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.