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
Firefox can execute the genome browser stored in your local disk opening the resulting HTML file. If you prefer to use other browser, you should perform the following actions:
(it should be executed to allow the accession to local files)
google-chrome --allow-file-access-from-files # with chromium execute: chromium-browser --allow-file-access-from-files
open -a Google\ Chrome --args --allow-file-access-from-files
Enable the develop menu using the preferences panel, under Advanced -> “Show develop menu in menu bar”
Then from the safari “Develop” menu, select “Disable local file restrictions”
It is also worth noting safari has some odd behavior with caches, so it is advisable to use the “Disable caches” option in the same menu; if you are editing & debugging using safari.
Run local application server
Another option is generate a D3GB server browsers and execute your own application server. The simplest probably is to use Python’s built-in http server.
If you have Python installed, it should be enough to run this from a command line:
python3 -m http.server
This will serve files from the current directory at localhost under port 8000: