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Bookmark widget

TL;DR: The bookmark widget stores genomic regions for quick navigation. Each bookmark is a single region (chromosome, start, end), shown as a colored highlight on the LGV; clicking one navigates a linear genome view (LGV) to it. Export bookmarks as a BED or TSV file, or import them back in.

The dropdown above the table filters bookmarks by assembly, and columns resize by dragging the grey divider lines.

Creating bookmarks

Click and drag on the top of any LGV and select "Bookmark region."

Create a bookmark by clicking and dragging the top of any LGV and selecting 'Bookmark region.' Open this view in JBrowse ↗

The steps behind the figure above, run against your own data.

  1. Open your genome: on the JBrowse Desktop start screen click Open new genome (or Show all available genomes to pick a hosted one).This figure uses hg19, loaded from a bgzip-compressed FASTA (.fa.gz + .fai + .gzi).
  2. Add your own track: File → Open track..., then paste a URL or choose a local file. This one needs a bgzip-compressed, tabix-indexed GFF3 (.gff.gz + .tbi).This figure uses “NCBI RefSeq genes (hg19)”.
  3. Type your region of interest into the location box and press Enter.This figure is at chr10:89,613,000-89,740,000.

Open this view in JBrowse Desktop ↗

Opens JBrowse Desktop (JBrowse Desktop 5.0+) at this view and saves it as a reopenable session — swap in your own files afterwards.

Nothing happens? Paste this link into Desktop's Open JBrowse Web link... (start screen, or File → Session):

https://jbrowse.org/code/jb2/main/?config=test_data%2Fconfig_demo.json&session=spec-%7B%22views%22%3A%5B%7B%22type%22%3A%22LinearGenomeView%22%2C%22assembly%22%3A%22hg19%22%2C%22loc%22%3A%22chr10%3A89%2C613%2C000-89%2C740%2C000%22%2C%22tracks%22%3A%5B%22ncbi_gff_hg19%22%5D%7D%5D%7D&sessionName=JBrowse+docs%3A+bookmark_widget_create

This session spec pastes after &session=spec- on any JBrowse Web instance.

{
  "views": [
    {
      "type": "LinearGenomeView",
      "assembly": "hg19",
      "loc": "chr10:89,613,000-89,740,000",
      "tracks": [
        "ncbi_gff_hg19"
      ]
    }
  ]
}

Loaded against config: test_data/config_demo.json

The same view with jbrowse-anywidget. Point the adapter at your own file.

from jbrowse_anywidget import LinearGenomeView, fetch_hub

view = LinearGenomeView(
    assembly=fetch_hub("hg19"),
    location="chr10:89,613,000-89,740,000",
)

view.add_track({
    "type": "FeatureTrack",
    "trackId": "my_track",
    "name": "My track",
    "assemblyNames": ["hg19"],
    "adapter": {"type": "Gff3TabixAdapter", "uri": "https://your-server/your-file"},
})

view  # display the widget

Hand this to a coding agent. It rebuilds the figure above headlessly, and the session file is then the thing to edit — swap an adapter uri for your own file and rerun.

cat > session.json <<'JSON'
{
  "views": [
    {
      "type": "LinearGenomeView",
      "assembly": "hg19",
      "loc": "chr10:89,613,000-89,740,000",
      "tracks": [
        "ncbi_gff_hg19"
      ]
    }
  ]
}
JSON

npx @jbrowse/capture --instance https://jbrowse.org/code/jb2/main/ \
  --config https://jbrowse.org/code/jb2/main/test_data/config_demo.json \
  --session session.json -o figure.png

Using JBrowse with AI agents covers the rest: hosted genomes to point it at, and why waiting for the render is the part that goes wrong.

A span of PTEN selected on the scalebar and bookmarked, the widget opened from the view menu, the row named, and the view sent elsewhere on chr10 before the row's link brings it back to the bookmarked span. Open the session this video starts in ↗

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.

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. Open this view in JBrowse ↗

The steps behind the figure above, run against your own data.

  1. Open your genome: on the JBrowse Desktop start screen click Open new genome (or Show all available genomes to pick a hosted one).This figure uses hg19, loaded from a bgzip-compressed FASTA (.fa.gz + .fai + .gzi).
  2. Add your own track: File → Open track..., then paste a URL or choose a local file. This one needs a bgzip-compressed, tabix-indexed GFF3 (.gff.gz + .tbi).This figure uses “NCBI RefSeq genes (hg19)”.
  3. Type your region of interest into the location box and press Enter.This figure is at chr1:1-20,000.

Open this view in JBrowse Desktop ↗

Opens JBrowse Desktop (JBrowse Desktop 5.0+) at this view and saves it as a reopenable session — swap in your own files afterwards.

Nothing happens? Paste this link into Desktop's Open JBrowse Web link... (start screen, or File → Session):

https://jbrowse.org/code/jb2/main/?config=test_data%2Fconfig_demo.json&session=spec-%7B%22views%22%3A%5B%7B%22type%22%3A%22LinearGenomeView%22%2C%22assembly%22%3A%22hg19%22%2C%22loc%22%3A%22chr1%3A1-20%2C000%22%2C%22tracks%22%3A%5B%22ncbi_gff_hg19%22%5D%7D%5D%7D&sessionName=JBrowse+docs%3A+bookmark_widget_edit_label

This session spec pastes after &session=spec- on any JBrowse Web instance.

{
  "views": [
    {
      "type": "LinearGenomeView",
      "assembly": "hg19",
      "loc": "chr1:1-20,000",
      "tracks": [
        "ncbi_gff_hg19"
      ]
    }
  ]
}

Loaded against config: test_data/config_demo.json

The same view with jbrowse-anywidget. Point the adapter at your own file.

from jbrowse_anywidget import LinearGenomeView, fetch_hub

view = LinearGenomeView(
    assembly=fetch_hub("hg19"),
    location="chr1:1-20,000",
)

view.add_track({
    "type": "FeatureTrack",
    "trackId": "my_track",
    "name": "My track",
    "assemblyNames": ["hg19"],
    "adapter": {"type": "Gff3TabixAdapter", "uri": "https://your-server/your-file"},
})

view  # display the widget

Hand this to a coding agent. It rebuilds the figure above headlessly, and the session file is then the thing to edit — swap an adapter uri for your own file and rerun.

cat > session.json <<'JSON'
{
  "views": [
    {
      "type": "LinearGenomeView",
      "assembly": "hg19",
      "loc": "chr1:1-20,000",
      "tracks": [
        "ncbi_gff_hg19"
      ]
    }
  ]
}
JSON

npx @jbrowse/capture --instance https://jbrowse.org/code/jb2/main/ \
  --config https://jbrowse.org/code/jb2/main/test_data/config_demo.json \
  --session session.json -o figure.png

Using JBrowse with AI agents covers the rest: hosted genomes to point it at, and why waiting for the render is the part that goes wrong.

Highlights

New bookmarks are assigned a highlight color by default. Change it in the Highlight field, or change several at once via "Edit colors" in the bookmark widget's menu.

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

Importing and exporting

Export bookmarks to a list of regions as a BED or TSV file, or import them from the same formats. Imported bookmarks are appended to your existing bookmarks.

Deleting bookmarks

Select bookmarks (see Selecting bookmarks) 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.

See also