Interpret and Navigate ChIP-Seq Tracks

Accessing Tracks

Access the Tracks Plot Page by selecting the Tracks icon on the top of your experiment page, or by selecting a ChIP Peak Results row for further exploration:


Introduction to Tracks

The Tracks Plot Page enables you to explore and compare peaks found in your ChIP-seq data. 

  • Each horizontal plot, called a "track", represents data positioned on a chromosome within a selected range. This interactive page displays multiple tracks, across the same region of a chromosome, allowing for comparisons between samples. Peak Tracks display peak heights and shape. Gene Tracks (displayed below the peak tracks) reveal gene positions in relation to the peaks.
  • Each Tracks Plot displays information for a selected region of your comparison (represented by the venn diagram) found on your Interactive Analysis page.


Significant Peaks

Significant peaks within your current Comparison and selected Venn Region, will be listed in the Significant Peaks Table at the bottom of the page. Click a row in this table to center your Tracks Plot on a selected row/peak.



Nearby Peaks

Peaks located near your selected significant peak may be viewed by clicking the Nearby Peaks Tab at the bottom of the page.

  • The Nearby Peaks Table displays:
    • Peaks visible in your Tracks Plot (pv, peaks visible)
    • The first 3 peaks before your Tracks Plot view begins (pb, peaks before)
    • The last 3 peaks after your Tracks Plot view ends. (pa, peaks after)

  • Clicking on a visible peak (vp) will cause the Range Finder to move to your selected peak position.
  • All visible peaks display  on their Nearby Peaks Table rows. Clicking on  will cause the Tracks Plot to redraw and center on the selected peak.
  • Clicking on the one of the Nearby Peaks Table rows located before or after your viewable range (bp, ap) will cause the Tracks Plot to redraw and center on your selected peak position
  • Conducting a search will display peaks in range within the Nearby Peaks Table.


Tracks Management

Line Chart (Stacked)

Selecting the Line Chart (Stacked) option from the Peaks Display Selector on the top left side of the page displays one combined track for each group.

Area Chart (Distinct)


Selecting the Area Chart (Distinct) option from the Peaks Display Selector on the top left side of the page displays each of your tracks individually. Group names are displayed vertically to the left of the tracks.

Disabling/Enabling Tracks

All tracks are enabled by default. To stop a track from displaying, uncheck the colored boxes that appear next to sample names on the on the left side of the page. Re-check the box to add a track back to your view.

Add Track/Group

Create a custom group by clicking the Add Track/Group Button on the left side of the page. Provide a name for your new group, and then drag your desired tracks from other groups into your new custom group.




Search for any gene of interest by typing the gene symbol into the Search Box located at the upper left side of the page.

Range Search for any desired chromosome range by entering the range into the Search Box. Ranges must be entered in the format chr#:start-end. For example: chr12:12000100 -13000200


Mouse Hover Features

Position Indicator The Position Indicator appears as you move your mouse along a track. This red vertical line indicates the location on the chromosome.
Gene Information

Information about each gene appears as you hover your mouse over Gene Tracks. Unfilled gene arrows indicates that the gene continues beyond the visible range of the current Tracks Plot.


Downloading Tracks Plot Images

Tracks Plot images are available for download by clicking the Button located at the upper right of the page.