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
Working with SVA genome browser
SVA provides an integrated genome browser, located at a "genome browser" panel:
1. The data for SVA genome browser
The data for the SVA genome browser (saved in a .gbb file) is separate from your project variant data (saved in a .bin file). The path for this .gbb file is specified in your project file (.gsap file) with this field: "[GenomeBrowserBuffer]=" .The genome browser .gbb file can be automatically generated from the supporting databases released with SVA, as long as you specified the "[GenomeBrowserBuffer]=" field in your project.
For you different projects with (1) the same genome build, and (2) the same number of chromosomes, you do not need to re-generate the .gbb file separately for each of these projects during the annotation, and may just use the existing .gbb file and leave the "[GenomeBrowserBufferSwitch]=on" statement. In this case SVA will directly load the existing .gbb genome browser buffer file.
For the whole genome build 36, the size of the corresponding .gbb file is around 1.5GB. For chromosome X only as in the example project, the size of the corresponding .gbb file is around 60MB.
2. Starting SVA genome browser
By default the SVA genome browser is not initiated when you load a project. The status of SVA genome browser is indicated in the status bar at the bottom of the genome browser panel (figures below).
There are several equivalent ways to start SVA genome browser:
3. Navigating in SVA genome browser
The SVA genome browser has to be started first for the navigation system to work. The SVA genome browser provides several navigation options (figure below). In the following table I list these options (top to bottom, left to right):
4. Select sections to display
Click on the "Select sections to display" button in the navigation tool bar (figure above), you will see a dialog like this:
This option allows you to select the displayed sections in the SVA genome browser.
5. A real example: search for the Factor VIII gene in the example project
Using the example project, we can use the searching for the Factor VIII (F8) gene as an example of interacting with the SVA genome browser.
Type in "F8" in the "gene symbol navigating" drop-down box, then click on ">Search gene" button at the right. It may take 30 seconds also for SVA to collect the data in this region. You will first see a note like this:
This indicates that SVA has found that the F8 gene on chromosome X, with three annotated transcripts (only one of them will be the most common, or 'canonical' transcript, which will be described later in this page). This note also gives the Ensembl stable ID and the coordinates for these three transcripts.
Then you will see that the SVA genome browser displays an image including several sections, described in the next page >>>
© 2011 Dongliang Ge, PhD.