Configuring a session
Welcome to the ComparativeBrowser wiki!
When the browser is first started you will be presented with an empty window as follows:
The first step to configure the genome browser is to identify the genomes you will be using. To do this select File -> Add Genome.
You will be presented with the following prompt:
where you can specify the identifier for the genome you will be using. To view multiple genomes in a single session simply use this menu to add additional genomes. Once you click Ok the main view window will be updated to include a new partition for the added genome, as shown below (here 3 genomes have been loaded):
Once at least one genome has been specified, you can start loading data tracks by going to the menu and selecting Tracks -> Load Track.
You will be presented with the following prompt:
Where you can select the files you wish to load, and the genome that they should be displayed relative to. Using this menu the browser can load BAM, BED, BW (big-wig), GTF format files. After loading some tracks for each genome and setting the viewed coordinates, the browser should look something like this:
To enable efficient access, some flat files (BED, GTF) are indexed before loading, so you may experience a delay the first time the file is loaded by the browser. The generated index is cached on disk, so these delays are avoided in subsequent sessions.
Once all your genomes have been loaded you can load whole genome alignments by going to the menu and selecting File->Load Alignments.
You will be presented with the following prompt:
that allows you to load pairwise alignments between the genomes in your session. Here, if the session has k genomes loaded, it is only necessary to load k-1 pairwise alignments such that all your genomes are mutually reachable. Consider the case where k=3, then there are 3 valid combinations of alignment files you can load at this window as depicted below.
Once the alignments are loaded the synteny overlay will be displayed:
If you have many genomes and tracks to load the configuration process can be tedious. If you frequently need the same session configured you can specify the configuration in a script. The steps outlined above each have an analogous representation in the script. The script is formed from a series of configuration commands executed in sequence. The list of available commands are:
load genome ()
load track ()
load alignment ()