Choosing a Region

Selecting by Chromosome

Genome cytoband selector.

Chromosome cytoband selector.

Cytoband data is specified during setup. The default is human hg38. A chromosome can be selected by clicking on it. Non-canonical chromosomes can be found in the Other selection box. A cytoband view of the selected chromosome is rendered. Clicking and dragging along the chromosome will select a specific region.

Note

Currently there is a limitation on the size of the region that can be viewed. Enabling arbitrarily large regions for viewing is a future goal.

Selecting by Gene

Gene annotations data is specified during setup. The gene search bar will search for any preloaded genes. The last four searches are saved as buttons.

Select by Gene.

Selecting by Coordinate

PangyPlot uses a coordinate system based on one of the reference paths embedded in the sequence graph. The primary coordinate system is specified during setup — typically using a reference genome such as hg38 or t2t for humans.

Selection methods above will fill the with a set of coordinates.

Coordinate section.

Enter coordinates

Manually enter or adjust the coordinate range.

Copy coordinates

Copy the current coordinate range.

Set flanking

Set the number of flanking base pairs to include.

Upstream flanking

Include flanking sequence upstream of the coordinate range.

Downstream flanking

Include flanking sequence downstream of the coordinate range.

Go

Retrieve and display the specified coordinate range.