Animations

Overview

This tutorial demonstrates several basic and useful features in Nucleome Browser. Note that there are a lot of GIF files on this page. We recommend you to view these examples using computers rather than cell phones.

Panel organization

Create a new panel

When the mouse hovers on the plus button (top-plus), you can choose to create a panel from the drop-down menu. You can also duplicate a panel by clicking the duplication button (panel-duplicate) in the configuration toolbar located on the top-right of the panel.

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Fig. 4 Create a new panel

Flexible layout

Nucleome Browser supports flexibly adjust the composition of panels. You can drag a panel to a different position by clicking the title of the panel, holding the mouse, and dragging it to the desired location. A grey box will indicate the final view of the panel. You can release the mouse to confirm it. Panels can also stack on each other if you drag a panel to another panel’s title region. The mouse will turn into a re-size tool when you hover on the boundary of panels. You can drag it to adjust the height or width of a panel.

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Fig. 5 Nucleome Browser supports a flexible layout to arrange multiple panels

Genome browser tutorial

Left-click to highlight & right-click to zoo in

Use the left button of the mouse to highlight on 1D or 2D genomic tracks. You can further move the highlighted region by dragging the highlighted region. Use right-click to zoom-into the highlighted region(s).

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Fig. 8 Highlight on 1D and 2D genomic tracks using mouse left button. Right click the highlighted region to zoom-into

Click annotation to highlight multiple regions

You can click a region in the bigBed track to highlight this region. If this region has a name (defined in the fourth column of the bed format), all the regions with the same name will be highlighted. Highlighted regions will synchronize across all connected panels.

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Fig. 9 Click on one region on the bed track. Other regions with the same annotation (name) will be highlighted

Interactive scatterplot tool

You can open the scatterplot tool by clicking the scatterplot button (gb-scatterplot). Each dot represents a genomic region with X-/Y-axis represent signals from different genomic tracks. You can then use the mouse to select dots and visualize their locations on the genome browser. Highlight regions on the genomic tracks will also show as highlighted dots in the scatterplot tool.

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Fig. 10 Use scatterplot tool to interactively explore genomic tracks

3D structure tutorial

Panning, Rotating, and Zooming in/out on the 3D structure

Pan: Press the Control key and use the left button of the mouse to move. Rotate: Click and hold the left button of the mouse to rotate the 3D strcuture. Zoom in/out: Use the center mouse wheel to zoom in or zoom out.

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Fig. 11 Use the mouse to manipulate 3D structure

Super-impose bigwig on 3D structure

First, open the configuration window of the genome browser panel and enable rendering color using bigwig by clicking the color-by-bigWig button (color-bigwig) in the 3D structure toolbar. Select a bigwig track from the genome browser panel and drag the track to the target box on the 3D structure panel.

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Click segment on the 3D structure to navigate

Enable clickable operation on 3D structure by clicking the pencil symbol on the the 3D structure toolbar (the button will become darker). Left-click the mouse on the 3D structure to navigate to that region.

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Fig. 12 Use the mouse to manipulate the 3D structure

Synchronized highlight between genome browser and the 3D structure

Highlighted regions are synchronized between the genome browser panel and the 3D structure panel.

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Fig. 13 Use the mouse to manipulate the 3D structure