Configuring graph-based tracks

Genome Browser graph-based tracks may be configured in a variety of ways to highlight different aspects of the displayed information. Some track types, such as BAM tracks and certain gene tracks, offer dynamic calculation of items in the current window to display a density graph where the height is proportional to the number of items mapped to each genomic position. The following information explains each of the available configuration options.

Display settings



Type of graph: The default "Bar" setting depicts the graph data using color-filled bars. To view the data as a series of points or lines, select the "Points" setting.

Track height (boxed in blue): To change the default display height of the graph in pixels, type in a value from within the indicated range.

Data view scaling (boxed in red): The default "Use vertical viewing range setting" option displays the data using the parameters specified in the Vertical viewing range setting. To configure the graph to automatically scale to a range defined by the minimum and maximum data points in the current view, select the "Auto-scale to data view" option. To keep the y=0 value in view at all times when Auto-scale is selected, set "Always include zero" to "ON".

Vertical viewing range (boxed in red): The min and max values specify the vertical portion of the graph that is displayed (default range is 30-70). These numbers can be used to set data threshold indicators. For example, to display only those GC values greater than 50 percent, set the min value to "50".

Transform function: Transforms the data points by the function selected in the drop-down menu. Usually the default setting is "None".

Windowing function: When a view is too large to show individual data values, the values must be combined to produce a plot point. This option specifies the combining function to be used (default is "Mean"):

Smoothing window: When set to a numerical value, this option determines the size, in pixels, of a smoothing window to be passed over the plot to smooth the edges of the bars or lines. This is equivalent to a trend line calculation on the graph. The default setting is "OFF".

Negate values: When checked, all values in the wiggle are negated, meaning that positive values become negative and vice-versa. This is useful for wiggles representing transcription or other activities on the minus strand. Be aware that wiggles with negative values are drawn in altColor not color as positive values are. The below image shows ENCODE RNA-seq data around two genes on different strands, SIRT1 and HERC4, with a minus signal track using Negate values to flip the wiggle display to emphasize that HERC4 expresses on the minus strand. This image also displays the signal graphed in points and a smoothing window of 16 pixels.

Draw y indicator lines (boxed in orange):

When you have finished making your configuration changes, click the Apply button to preview your changes, or click the Submit button to return to the annotation track display page.

Annotation track display modes

Each annotation track within the window may have up to five display modes:

Dense
The track is displayed with all features collapsed into a single line. The darker the line color the greater the wiggle value at that location.
Wiggle in dense display
Squish
The track is displayed with all the features collapsed into a single line, much like the dense display mode with greater compression.
Pack
The track displays the wiggle value associated with each annotation feature creating a histogram-like image, much like the full display mode with greater compression.
Full
The track displays the wiggle value associated with each annotation feature creating a histogram-like image.
Hide
The track is not displayed at all. To hide all the annotation tracks, click the hide all button.

Overlay method

Note that not all graph-based tracks include the Overlay options.

Transparent
This setting displays the colored transparent graphs of multiple subtracks overlayed in the same vertical space.
Solid
This setting displays the colored opaque graphs of multiple subtracks overlayed in the same vertical space.
Stacked
This setting displays each graph stacked on top of each other where the high point of the graph is the sum of all the values.
None
This setting displays each graph in its own vertical space.