Helpful Tips and Tricks

Search regions or identifiers: Input a region specified like ‘10:31610549-31818742‘ or ‘ZEB1‘, then click

Search free text on gene tracks: Input a word to search in browser, then click

Hide/Show track: Click on a track’s name to hide/show it.

Move right/left: Drag n’ drop (horizontal) or right and left arrows to advance in the browser.

Reorder tacks: Drag n’ drop (vertical) to reorder tracks.

Modify max/min represented values: Click on a max/min value track’s scale to change it.

Show full feature information: Click on genes, exons, domains or VCF glyphs will display a window with information about the feature.

Show additional information: Hover on the feature glyphs for additional information.

View VCF annotation explanation: Hover on the acronyms in the VCF’s annotation window for its description.

Create a local/server Genome Browser

Genome browser can be created in two versions: Local and Server. Server version creates a folder with files that can be added to an Apache server. Copy this folder to your root Apache applications path and change directory permissions to enable reading and execution by Apache user.

Where is stored the graph? and How to open it?

Resulting graphs are stored in a new folder created in the R working directory. The name of this folder can be passed as parameter. This folder contains one file named “index.html” that should be opened to view resulting graph.

How to view a genome browser stored in your local disk

Any web browser can execute the genome browser stored in your local disk opening the resulting HTML file.