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
Annotating a project
After you create or open a project, click on button "ANNOTATE" in the "Project Builder" dialog to perform the main function annotation.
Again, I feel necessary to mention this important note one more time - sorry for being a nagger:
What does this process do?
This annotation process does three things:
Sometimes, there will be a log file called "[YOUR SVA PROJECT FILE].exception.log" generated in your project folder (see figure below). This file saves all the genetic variant records in an unrecognizable format to SVA. If you include contigs not yet mapped to a chromosome in your reference sequence database when performing the alignment, those genetic variant mapped to contigs will, for example, be included in this file and will not be annotated for genomic functional context.
The function annotation may take 3-4 hours to complete for around 10 million variants, based on the computer we have been using. After the annotation is done, you will then be able to summarize and analyze the annotated data.
© 2011 Dongliang Ge, PhD.