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
Updating annotation databases
There are two different types of updates of SVA annotation databases:
(1) Main update: update of hyman reference genome. We will release new SVA package when new genome builld becomes available, and post it onto the SVA website as soon as we can. Users need to re-download the SVA package to effect this update. There are currently two different releases of SVA packages regarding the main updates: build 36 (Ensembl version 50_36l) and build 37 (Ensembl version 61_37f).
(2) Minor update: update of gene annotation databases within a given genome build. Users are suggested to directly download the annotation databases and put it into the relevant SVA directories, following the instructions below, to effect these updates. We will also maintain an update following the Ensembl releases in the standard SVA release. However, this update will not be made following each update of Ensembl core databases. Therefore, users are strongly encouraged to perform this update themselves when they desire.
Here is how to perform the minor update:
(2.1) Locate and download the Ensembl annotation databases.
Visit Ensembl's database downloading ftp site:
Locate the directories for human databases:
homo_sapiens_variation_[ENSEMBL VERSION] (replace ENSEMBL VERSION with correct database versions, for example 61_37f)
Users need to download the following data files from these directories. Please note you will need to extract the downloaded .gz files to flat text files.
If for "variation_feature" and "allele"there is only one file instead of two "001" and "002" files, rename the download file to end with ".001.txt" , and then create an empty file with the name ended with ".002.txt".
(2.2) Create a relevant SVA database directory
Locate your SVA installation directory. Then create your SVA annotation database directory. Typically, it should be at:
[YOUR SVA INSTALLATION DIRECTORY]/datasource/ensembl/[YOUR DATABASE VERSION]
Put all the downloaded files from step 1 into this directory.
(2.3) Use the updated annotation databases in your next SVA annotation job
In your SVA .gsap script file, you need to specify to use the newly updated data files to effect the update. Specifically, you need to update these statements:
(2.4) Alternatively, use [USERTRACK] option to include user annotation track
You may want to include user annotation tracks in GFF3 or BED format to perform annotations in addition to the core annotation. To do this, include the following statements:
[USERTRACK]= [YOUR TRACK NAME] , [YOUR TRACK FILE PATH].gff3
[USERTRACK]= [YOUR TRACK NAME] , [YOUR TRACK FILE PATH].bed
If your gene annotation files are in GTF format, they can be conveniently converted into GFF3 format using this online tool:
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© 2011 Dongliang Ge, PhD.