1. Add/remove genomic feature tracks
  2. Configure track rendering
  3. Custom genomic feature tracks
  4. Other operations with genomic feature tracks

Add/remove genomic feature tracks

First step will be deciding which tracks to be listed. Go to control panel at "Tracks" → "Genomic features":

The table "your collection of genomic feature tracks" holds the list of tracks you can work with. Each row corresponds to a track, displaying track name, file type, mode operator, and removal sign. To add more tracks to this list, click button :

A new panel pops out where you can see the entire inventory of genomic feature tracks provided by the Browser. This panel contains two parts, the left part is a list of group names. Clicking one will reveal that group of genomic feature tracks on the right part of the panel. To select a track from the inventory and add to your list, click on the track name. In the example below, two gene tracks have been selected and added to the list:

Once you're done, click at anywhere else on the page to dismiss the track selection panel.

To remove tracks you don't need, click ✕ sign in the list. Removed tracks can always be added back again.

In addition, Browser tracks are organized into "parent-child" relationship. Click the arrow ↓ following name of parent track to toggle display of its children tracks:

You can change display of the tracks in Browser via drop-down menus in the track list table. For genomic feature tracks with positional data (such as genes), three display modes are available: thin, full, density. In following example, "UCSC genes" track is in full mode, "SINE" track is in thin mode, and "LINE" track is in density mode.

When the track is in "thin" or "full" modes, clicking on one genomic feature a tooltip will pop out displaying some information on the clicked item:

Right click on the genomic feature track image will invoke a context menu. You can easily switch display mode (full/thin/density) via menu options:

This "tooltip function" only applies to genomic features with positional data, but not those with quatitative data (such as "GC percent" tracks).

Configure track rendering

Select wrench option in the context menu on a genomic feature track:

A configuration panel will appear in floating toolbox. But the contents in the panel will be somewhat different depend on the type of track being configured:

Tracks in thin/full mode This is positional data tracks with each genomic feature plotted separately. The configuration panel will look like:
As indicated, you can configure font and plotting color for the track.

Tracks in density mode When tracks are switched from thin/full modes to density mode, quantitative (density) data will be plotted, and the configuration panel will change as well to adapt:
It is similar with the configuration panel for genome heatmap tracks. Track's Y-axis can be defined in three ways: automatic, fixed, and percentile threshold. Track height and plotting color can also be changed. For detailed explanation, please refer to section of configuration in genome heatmap.

Quantitative tracks Genomic feature tracks with quantitative data will only be plotted in wiggle style. Examples include GC percent, and sequence conservation score. The configuration panel of such tracks look like:
As arbitrary data could be contained in quantitative tracks, compared with only positive values for density tracks, some more options are provided in its configuration panel, including changing plot color for negative values.

All such configurations can be saved in session.

Custom genomic feature tracks

The Browser supports displaying custom genomic feature data (positional data) in form of custom bigBed tracks. Please refer to that chapter for detailed information.

Other operations with genomic feature tracks

Change order of appearance you can move tracks to top/bottom of the stack through respective menu options.

Juxtaposition This function can only be applied on BED-style tracks, which pulls and places data on the items in this track together for focusing or contrasting. Please refer to chapter of genomic juxtaposition for details.

Correlation Correlation of heatmap track values against genomic feature tracks can be performed. The genomic feature track must contains quantitative data, or in density mode. Refer to chapter of correlation for details.

Gene Plot This function only applies to custom bigBed tracks. Refer to chapter of gene plot for details.


Last modifed: 12/30/2011