Peak track

The main output of the Transcription Factor ChIP-Seq tool is an annotation track containing the peaks. The table view (figure 36.12) can be opened by clicking on the table icon (Image table) in the lower left corner of the peak annotation track. For each peak, it contains:

For more details on some of the values above, see Applying peak shape filters to call peaks. Information about the genes located upstream and downstream of the peaks can be added to the table by using Annotate with Nearby Information.

The peak annotation track is most informative when combined with the read mapping in a track list (figure 36.12), see Track lists for details.

Image NRSF_peak
Figure 36.12: Top: Track list containing the mapped reads, the Peak track annotated with nearby genes, and the Peak shape score track. Bottom: Table view of the Peak track. Clicking a peak in the table will update the track list to show the selected peak.