Customizing the View

Controls

Chromosome view can be customized by using the control panel on the left. The Group data by option specifies the number of Alignments tracks. The Attribute and Order by controls show options depending on the current analysis. In order for any change to take place, push the Apply button.

All

All will result in only one track, with all the samples on it.

Sample

Sample creates one track per sample, with option to Order by sample attribute.

Attribute

Attribute produces one Alignments track per level of the Attribute (i.e. one track per group).

Customize track colors

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

Annotate amino acids by

Annotate amino acids by option controls the appearance of the Amino acids track and allows you to pick the transcript database that will be used to plot codons. It can be customized by clicking setting icon on Amino acids track. In the Configuration dialog, select an annotation file from the Annotate amino acids by drop down list. The drop down list shows annotation files associated with the current genome build.

Color by

Color by option affects the colouring of the Alignments track and Isoform proportion track. It can be customized by clicking setting icon on aforementioned tracks. In the Configuration dialog, Sample, Base, and Match options are present by default, if attributes have been assigned to samples, they will appear in the drop-down list. In figure below, that are the "Type" and "Subject ID" attributes.

Color by Sample

When Sample is selected from the Color by drop-down list, individual samples will be shown on the track, each sample being given a different colour.

Color by a sample attribute

When a sample attribute is selected from the Color by drop-down list, different colors will be used to depict levels of the selected sample attribute (as present in the Metadata tab).

Color by Base

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

Color by Match

Color by Match option can be used to quickly identify mismatches against the reference genome. A matching base is coloured in blue, while mismatch bases are colored in yellow.

Histogram type

Histogram type changes the presentation of the Alignments track. It is customizable on Configuration dialog invoked on the Alignment track, and should be used in conjunction with the Group data by and Color by tracks to get the desired visualisation.

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

To show the average coverage per locus, switch histogram type to Average and leave Color by as is (i.e. by group). 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. Note the difference in y-axis range in figure below compare to the figure when the histogram type was set to Sum.

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). The example in figure below 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.

Y-axis max

The maximum of the y-axis of Alignments tracks is set by Y axis max option in Configuration dialog invoked from the Alignments track. When using Project max, all the tracks have the same Y axis maximum, which depends on the sample with the highest coverage. On the other hand, Track max uses independent Y axis maximum for each track.

Project max

Track max

Split by strand

To view the histogram grouped by the specific strand that they've mapped to, click the Split by strand checkbox in the Configuration dialog on Alignement track. This displays the forward reads at the top half of the track and the reverse reads on the bottom half of the track. This track can be helpful in studies such as ChIP-Seq, where strand-specific read distributions can display hallmarks of DNA-protein interactions.

Transcript label

You can use the Transcript label option to specify labels on the reference transcript track and Isoform proportion track. Click setting icon on aforementioned tracks to open the Configuration dialog. Both transcript database and Isoform proportion tracks of Short sequencing reads can be coloured by strand (Reads pileup color: Strand) or by base (Reads pileup color: Base).

Transcript label: Gene

Transcript label: Transcript

Reads pileup and probe color

Reads pileup track can be displayed on Chromosome View by selecting Short Sequencng Reads data from Select tracks tool. Click setting icon on the Reads pileup track to open Configuration dialog, two options are available to color the reads pileup: strand, base.

Reads pileup color: Strand

Reads pileup color: Base

Probe color control customizes the appearance of Probe intensities track. When set to Intensity, the color of a probe reflects its intensity, using a 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 is in sky blue.

Probe color: Intensity

Probe color: Strand

Variant database

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

Track Order

The position of the tracks on canvas can be controlled by using the Track order tool on the left of each track. 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. Below shows the Cytoband track pinnned to the top of the canvas. To unpin a track, click on the pin icon .

To pin a track, click the green arrows to pin a track to the top or bottom of the view. When you mouse over an arrow, the new position of the track will be highlighted on the canvas; click on the arrow to accept.

A track can be hidden (meaning it will not be visible) by selecting the minus icon.

Hidden tracks can be unhidden by selecting the plus icon at Hidden tracks section on the left panel.

The tracks can be reordered by drag and drop.

Selection Details

At the bottom of the control panel you will find the Selection details section. It is used to display information on the element selected on the canvas (using the Pointer mode). Example below shows details of a microarray probe. Note the two link-outs ("Browse on UCSC" and "BLAST this sequence")