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Chromosome view can be customized by using the control panel on the left (Figure 371). The Attribute and Order By controls show options depending on the current project, while the content of the Annotate amino acids control depends on the annotation files associated with the current genome build in the Library File Management. In order for any change to take place, push the Apply button.

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The first option, Group data by, specifies the number of Alignments tracks (Figure 382). All will result in only one track, with all the samples on it. Sample creates one track per sample, while Attribute produces one Alignments track per level of the Attribute (i.e. one track per group). 

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Annotate amino acids by controls the appearance of the Amino acids track and allows you to pick the transcript database that will be used to plot codons (Figure 393). The drop down list shows the databases currently available for the selected genome (additional databases can be added via Library File Management). 

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Color by option affects the colouring of the Alignments track and Isoform proportion track. When Sample is selected from the drop-down list, individual samples will be shown on the aforementioned tracks, each sample being given a different colour. If attributes were assigned to samples, they will also be visible in the Color by drop-down (Figure 404) and you will be able to highlight levels of the selected attribute (Figure 415).

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The effect of the option to Color by Base can be seen with high power magnification (Figure 426). Individual base calls are highlighted by different colours. When that option is chosen at low power magnification, all the bases are shown in grey.

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The maximum of the y-axis of Alignments tracks is set by Read histogram Y axis scales option (Figure 437). When using Independent, the y-axis for each track is set individually, based on the maximum within that sample. On the other hand, Linked uses the maximum across all the samples and uses that value as the maximum for all. 

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When set to Sum, the Read histogram type shows the sum of base calls at each position, i.e. total coverage per position. Figure 44 8 shows an Alignments track with three samples. With the Sum option, number the number of reads at each base in each sample is added and displayed. Contribution The contribution of individual samples is not visible, since visible since the track is Colored by Group (but that would make sense in this example).

To show the average coverage per locus, switch Read histogram type to Average and leave Color by as is (i.e. by group) (Figure 459). With this setting, Chromosome view will calculate the average by dividing the total coverage per locus by the number of samples. Note that using Color by Sample would not make sense here. Although Figure 44 8 looks quite like Figure 437, the y-axis range is different.

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Finally, the option Overlay is useful if you want to directly compare base counts over several samples (or groups) as each will be represented by a line (i.e. no stacking). Example The example in Figure 46 10 is based on microarray data, showing three groups on the same Alignments track. The red group has the highest base counts, while the counts in the blue group are much lower.

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You can use the Transcript label selector to specify labels on the reference transcript track and Isoform proportion track (Figure 4711).

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Probe color control customizes the appearance of Probe intensities track (Figure 4913). When set to Intensity, colour the color of a probe reflects its intensity, using a colour color gradient from white (low) to admiral (high). Alternatively, when Strand is turned on, probes on the reverse strand are in parakeet green, while probe on the forward strand are is in sky blue.

If a variant database is available for the current genome, the variants can be added to the Reference genome track (Figure 33). To show the variants, point the Variant database control to the database of your choice.

To change any of the colours on the canvas, use the Customize track colors tool. A resulting dialog will help you to pick another color (drop-down button opens the colour-picker) (Figure 5014).

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The position of the tracks on canvas can be controlled by using the Track order tool. If you want a track to be visible all the time, i.e. while scrolling up or down, pin it to the top or to the bottom. Figure 51 15 shows Cytoband track pinnned to the top of the canvas and Reference genome track pinned to the bottom of the canvas. To unpin a track, click on the pin icon ( ). The track will be unpinned and a message No tracks are pinnned to the top / bottom will appear. To pin a track, drag the track name to the No tracks… message. Alternatively, you can use the green arrows ( ) to pin a track. When you mouse over an arrow, the new position of the track will be highlighted on the canvas; click on the arrow to accept.

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At the bottom of the control panel you will find the Selection details section (Figure 5216). It is used to display information on the element selected on the canvas (using the Pointer mode).

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