From the GSA task report, we can browse to any gene in the Chromosome view.

• Click  in the SELENOM row to open Chromosome view (Figure 1)
  
  

A new tab will open showing SELENOM in the Chromosome view (Figure 2).

Chromosome View shows reference genome, annotation, and data set information together aligned at genomic coordinates. 

Each track has Configure track  and Move track  buttons that can be used to modify each track. 

The top track shows average number of total count normalized reads for each of the three treatment groups in a stacked histogram. The second track shows the RefSeq annotation.

We can add tracks from any data node using Select Tracks.

• Click Select tracks

A pop-up dialog showing the pipeline allows us to choose which data to display as tracks in Chromosome view (Figure 3).

• Click Reads pileup under Aligned reads on the left-hand side of the dialog 
• Click Display tracks to make the change

The reads pileup track is now included (Figure 4).

With multiple tracks, it may be useful to pin a track to the top so we can scroll down the reads pileup track without losing sight of the Alignments or RefSeq tracks. 

• Click  next to the Alignments track
• Click  to pin the track to the top 
• Repeat for RefSeq Transcripts 
• Scroll down to view individual reads 

Selecting a read brings up detailed information about the read in the selection details panel (Figure 5).

To learn more about Chromosome view, please consult the Chromosome View user guide.