bigBed file generator

One shortcoming of "Gene set view" function is that you can't view too many genes at one time, say, >200 genes. In order to overcome this, the "bigBed file generator" is written, which allows you to submit arbitrary number of genes/coordinates and make a bigBed file which gives you wide range of browsing options once it's up as a custom track.

The bigBed file generator function interface can be found at "Miscellaneous functions" tab:

Enter a list of gene names or coordinates into the text area and you are good to go! Of course you can change your idea and select different part of genes to be used by clicking "Change" button:

The "gene part selector" panel will appears:

Click button to generate bigBed file, file URL will be given:

Finally, you can click button under the file URL and put it up as custom bigBed track instantly:

Have fun browsing!

User interface revised

2010 - 08 - 25

The navigation bar now has 3 button groups (identified by different background color and downward arrow): Genomic view, Tracks, Statistic functions. In a nut shell, "genomic view" defines components of horizontal axis of genome heatmap, and "Tracks" defines components of vertical axis. They are independent of each other.

Clicking "Genomic view" button will reveal the three buttons it contains:

Go to the "Gene set view", which is displayed by default when page is loaded, following panel will appear. "Custom gene set" and "KEGG pathway" function interface are in separate boxes:

After gene set submission, a panel will be shown containing available operations on the displayed gene set (some functions are yet to be released):

It has been made explicit that the browser would operate in one of four modes:

viewing genome juxtaposition on genomic features (server provided, curated source, or custom bigBed file) gene set view (on custom gene set, or KEGG pathway)

unassembled contigs A bit of restriction will apply to switching between last 3 modes, in that user has to cancel current mode to go back to genome view, and change to the new mode. For example, if user is doing gene set view, if she clicks on "Genomic juxtaposing", she will see:

The "Genomic juxtaposing" panel looks similar as "Gene set view", and provides interface to server/custom bigBed file juxtaposition functions:

And finally, the "Contig view" function interface has been made a bit more self-explanatory, highlighting the two possible ways to select contigs for viewing:

Configuring decorative tracks

2010 - 08 - 22

Right click on genomic feature track/P-value track/pairwise comp track, the option with wrench icon allows you to configure plotting style of such tracks:

A panel will appear in floating toolbox with drop down menus and color buttons to play with. Make changes and the track image will be redrawn immediately:

Also, go to "Config & Misc" > "Customize browser display", you will find options to change genomic feature track plotting styles. All options are same as those in toolbox, but this will change appearance of all tracks, and serves as default style.