Bookmark widget

The bookmark widget stores genomic regions for easy navigation. Each bookmark is a single region (chromosome, start, end); clicking one navigates a linear genome view to it.

The bookmark widget can be accessed via the Tools menu, or in the view menu 'Bookmarks' submenu.
The bookmark widget can be accessed via the Tools menu, or in the view menu 'Bookmarks' submenu.

The dropdown menu above the table of bookmarks can be used to view a subset of all assemblies with bookmarks.

Resize the columns of the table by clicking and dragging the grey lines above the table.

Creating bookmarks

Bookmarks can be created by clicking and dragging on the top of any linear genome view and selecting "Bookmark region."

Create a bookmark by clicking and dragging the top of any LGV and select 'Bookmark region.'
Create a bookmark by clicking and dragging the top of any LGV and select 'Bookmark region.'

Keyboard shortcuts

  • Create a bookmark: CTRL/CMD + Shift + D
  • Navigate to the most recently created bookmark: CTRL/CMD + Shift + M

Selecting bookmarks

Use the checkboxes to the left of the table to select bookmarks for bulk export, sharing, deletion, or editing.

Select your bookmarks of interest using the left checkboxes.
Select your bookmarks of interest using the left checkboxes.

Labels and highlights

Add a label to a bookmarked region by clicking the label field and typing, or double-clicking to open a dialog. Labels are saved and exported with bookmarks, and displayed on the LGV via highlights.

Create a label in the bookmarks widget, and it can be viewed on the LGV.
Create a label in the bookmarks widget, and it can be viewed on the LGV.

Highlights

New bookmarks are assigned a highlight color by default. You can change it directly in the Highlight field, or change multiple bookmarks in bulk via the hamburger menu → "Edit colors".

Highlight colors can be modified in the bookmarks widget.
Highlight colors can be modified in the bookmarks widget.

Highlights and labels can be toggled app-wide (via "Edit colors" menu) or per-view (via the view menu → "Bookmarks").

Sharing bookmarks

Select bookmarks with the checkboxes and click "Share" to get a URL you can send to collaborators or paste into the Import form described below.

Bookmarks can be shared using the Share option in the bookmarks widget.
Bookmarks can be shared using the Share option in the bookmarks widget.

Exporting bookmarks

You can export bookmarks into a list of regions as a BED or TSV file.

Exporting a list of regions to a TSV file.
Exporting a list of regions to a TSV file.

Importing bookmarks

You can import bookmarks from a list of regions in a BED or TSV file.

Importing a list of regions from a BED file.
Importing a list of regions from a BED file.

You can also import from a share link generated via the Sharing bookmarks section above.

Imported bookmarks are appended to your existing bookmarks.

Deleting bookmarks

Select bookmarks with the left checkboxes and press "Delete" in the widget menu to remove them.

Bookmark persistence

Bookmarks persist in browser localStorage, keyed to the URL JBrowse is hosted on. Only bookmarks valid for the currently loaded assemblies are shown.