From the GSA the DESeq2 task report, we can browse to any gene in the Chromosome view.

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

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

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

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

• Click Select Select tracks

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

• Select Click Reads pileup under Align Aligned reads on the left-hand side of the dialog 
• Select 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. 

• Select Image Removed next to the Alignments track
• Select Image Removed to pin the track to the top 
• Repeat for RefSeq
• 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.

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