Using this software0. For impatient users
1. Data inputs
2. Create a project
3. Annotate a project
Using user annotation track
4. Filter for quality scores
5. Main user interface
6. SVA genome browser
7. SVA tables
8. Selecting genes or regions
Bio-pathway or GO
Fisher's exact test
10. Exome or targeted capture sequencing
SVA is a JAVA program, designed to run on a LINUX platform with a 64-bit JAVA environment installed. SVA was designed to be a LINUX desktop software tool.
Please follow these steps in installing SVA:
(1) If you receive SVA release in a compressed package, decompress it to a directory. This can be done by (for a bz2 package):
(2) Copy the whole decompressed SVA package to your desired installation directory [YOUR SVA DIR].
(3) There is a SequenceVariantAnalyzer.sh script in the SVA package. This file has only two lines of scripts in it:
Replace the " [SVR DIR]" with your installation directory [YOUR SVA DIR].
(4) Make this script executable:
(5) Now you should be able to run the graphial user interface (GUI) of SVA:
(6) There is a svacmd.sh script in the SVA package. This file starts like this:
Replace the " [YOUR SVA INSTALLATION DIRECTORY]" with your installation directory [YOUR SVA DIR].
(7) Make this script executable:
(8) Now you should be able to run the command line tool of SVA:
The command line tool takes two parameters: 1. The amount of memory (RAM) you would like to allocate to SVA in megabytes (MB), and 2. The absolute, or canonical path of your SVA .gsap project file. You can create your .gsap project by copying and modifying the example project file.
It is very important to use the absolute, or canonical path of your SVA .gsap project file as the second parameter. The absolute path must start from the root (/), for example, '/user/MyName/Work/MyFile.gsap'. This is true even you are currently at your working directory and a relative path './[your file]' works for other programs. The SVA command line tool only recognizes the absolute, or canonical path of your SVA .gsap project file.
(9) There is a tmp directory under the installation directory [YOUR SVA DIR]: [YOUR SVA DIR]/tmp
Please make sure that the SVA user has write permission to this directory for its normal functioning.
1. As you can see from this process, SVA needs to start from its installation directory. - This merely was set for consistence with earlier behaviors of JAVA programs on a Mac.
2. You can easily set up a desktop shortcut for starting SVA. Here is an example. Again, you need to replace the " [SVR DIR]" with your installation directory [YOUR SVA DIR].
3. If you access using X server from a Windows PC, you need to follow the instructions of your X server to establish the X connection first.
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© 2011 Dongliang Ge, PhD.