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From the GSA task report, we can browse to any gene in the Chromosome Viewview.
- Select View view (Figure 1)
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A new tab will open showing SELM in the Chromosome View view (Figure 2).
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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 (Figure prev.) 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.
- Select Select tracks
A pop-up dialog showing the pipeline allows us to choose which data to display as tracks in Chromosome Viewview (Figure 3).
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- Select Reads pileup under Align reads on the left-hand side of the dialog
- Select Display tracks to make the change
The reads pileup track is now included (Figure 4).
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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 next to the Alignments track
- Select 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).
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To learn more about Chromosome Viewview, please consult the Chromosome View user guide.
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