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Sequence Viewer Tutorial

The Sequence Viewer displays annotations and expression data in context of the genomic sequence. The interface is similar to other genome browsers and is designed to follow familiar intuitive controls. To assist with collaboration, all configuration changes to the viewer are recorded in the URL so it can be copied and sent to another user.

Controls

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Interaction with the sequence viewer is based on common navigation elements.

Pan
Click and drag on the tracks to pan left and right across the sequence

Zoom
Use the mouse scroll wheel to zoom in and out

Sort
You can reorder tracks by clicking on the left item bar and dragging the track into position

Resize
Resize handles along the bottom edge and bottom right corner allow changing the height of tracks.

Region Navigator
The top track displays the sequence length, currently selected region and fields for the current view position. You can click and drag the current region or type in a new position to update the view.

Tracks

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Features
The features track displays genes and other genomic features. Clicking on a feature in the track will open a menu window with more details about the feature and links to expression and annotation data.

Sequence
The sequence track has two levels of display.

When < 10000 bases are in view, each individual base will be rendered and colored red, green, blue, and orange for A, T, C, and G respectively.

When > 10000 bases are in view, GC - content will be drawn with a line graph. The blue line represents the average GC content in the region calculated from a 100bp window. Orange lines represent the min and max GC content.

Reads
The reads track display read alignments in forward and reverse orientation. Forward and Revers reads can be colored separately. Paired reads are connected with a thin black line. Read gaps (generally from introns) are displayed with a thin colored line.

Density
The density track displays a count of reads at each base. This scale of density is global by default. Each track uses a y-scale based on the maximum of all open tracks. Each track can be configured to use a local track scale or custom value.

Track Menu

Each track has a control menu in the top right corner. The options in this menu are described in detail below.

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Select Track Region
Sv select seq 8946fdc8b4b6e1d2fb9f6e23ec76cd788fbb5db7d2d28c06df442df99f58b678 The target icon opens a submenu with controls from selecting a region of sequence. Click and drag along the panel or type in the region you are interested in. Then, you can open this selection for more details based on the track type.

  • Sequence: Displays a FASTA formatted result of sequence from the selected region

  • Features: Count of feature types in region

  • Reads: Displays a Read mapping table containing counts of reads aligned in the selected region. The table includes signle reads, paired reads, total count and the overall total mapped reads in the sample.


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Configuration
The gear icon opens a configuration menu for customizing each track. This includes color, height and axis settings.

Details
The [i] icon opens a window with detailed information for the selected track.

Close
The [X] icon closes the track removing it from view.