Skip to main content

A grammar of graphics over a BED (RepeatMasker Alu age)

JBrowse v5 beta

The tutorials target the JBrowse v5 beta, and the v4.3.0 release on the download page lacks some of what they show. To install the beta of JBrowse Web, run npm install -g @jbrowse/cli@next, then jbrowse create jbrowse2 --branch v5.0.0-beta.21. Desktop beta builds for Linux and macOS are on the releases page; the Windows build waits on code signing.

RepeatMasker annotates Alu, a primate-specific repeat family, and its milliDiv column records each copy's divergence from its subfamily consensus, in tenths of a percent. Divergence grows with time, so the column is an age, and the subfamily name (AluJ, AluS, AluY, oldest to youngest) is a coarser one. We ask where along chromosome 1 the young copies sit. We:

  • load the Alu rows of a RepeatMasker BED as a LinearMarkDisplay, one bar per copy with milliDiv as its height and its lineage as its color
  • bin and count the copies per window when zoomed out, with AluY's count over the total
  • count copies per kilobase over a whole chromosome into a bigWig with jbrowse make-density
  • plot the AluY share per megabase as a two-color bar track under that density

LinearMarkDisplay turns the columns of a feature file into plots from a JSON marks list. It is experimental, and its config shape may change.

Prerequisites

  • a JBrowse to open the figures' sessions in (Web or Desktop)
  • htslib (bgzip, tabix)
  • Node.js and the JBrowse CLI, for jbrowse make-density
  • python3, standard library only, for the per-megabase counts
  • bedGraphToBigWig from the UCSC utilities, which make-density runs
# Debian/Ubuntu
sudo apt install tabix nodejs samtools
# or conda, which has every tool above
conda install -c bioconda -c conda-forge htslib nodejs ucsc-bedgraphtobigwig \
  samtools
# or Linux x86_64 binaries for the tools apt lacks
wget -P ~/.local/bin \
  https://hgdownload.soe.ucsc.edu/admin/exe/linux.x86_64/bedGraphToBigWig
chmod +x ~/.local/bin/bedGraphToBigWig
# any platform
npm install -g @jbrowse/cli@next

The data

UCSC's hg38 RepeatMasker table, rehosted by genomes.jbrowse.org's hg38 with the Alu rows cut out.

You don't need these files to follow the page: the track configs below read the hosted results. The build script fetches them to rebuild those results. The build script takes your own RepeatMasker BED and genome FASTA as arguments and runs the same steps on them.

What it is File
RepeatMasker, UCSC's rmsk table as BED with a column header rmsk.bed.gz
Reference lengths, for the bigWig header hg38.chrom.sizes

Plotting each Alu copy's divergence at one locus

We'll load hg38, the assembly the RepeatMasker coordinates are on.

Goes in the assemblies array of config.json. See Assemblies.

{
  "name": "hg38",
  "uri": "https://jbrowse.org/genomes/GRCh38/fasta/hg38.prefix.fa.gz",
  "refNameAliases": {
    "uri": "https://s3.amazonaws.com/jbrowse.org/genomes/GRCh38/hg38_aliases.txt"
  },
  "cytobands": "https://jbrowse.org/genomes/GRCh38/cytoBand.txt"
}

Edits config.json in the current folder, creating it if there is none. See JBrowse CLI with Desktop.

jbrowse add-assembly https://jbrowse.org/genomes/GRCh38/fasta/hg38.prefix.fa.gz \
  --name hg38 \
  --refNameAliases https://s3.amazonaws.com/jbrowse.org/genomes/GRCh38/hg38_aliases.txt \
  --config '{"cytobands":"https://jbrowse.org/genomes/GRCh38/cytoBand.txt"}'

hg38 is one of the genomes JBrowse Desktop hosts, with gene tracks already set up: on the start screen click Browse hosted genomes and pick it. To load the files of this config instead:

In JBrowse Desktop, Open your own genome on the start screen (or File → Open genome... in a session), then Open from a URL and paste, one per line:

https://jbrowse.org/genomes/GRCh38/fasta/hg38.prefix.fa.gz
https://jbrowse.org/genomes/GRCh38/fasta/hg38.prefix.fa.gz.fai
https://jbrowse.org/genomes/GRCh38/fasta/hg38.prefix.fa.gz.gzi

JBrowse reads the format off the file name. Then fill in:

  • Genome name: hg38
  • refName aliases (under More options): https://s3.amazonaws.com/jbrowse.org/genomes/GRCh38/hg38_aliases.txt
  • cytobands (under More options): https://jbrowse.org/genomes/GRCh38/cytoBand.txt

The track reads one family's rows of a RepeatMasker BED. For a genome of your own, RepeatMasker's .out file lists class and family as one class/family field, and splitting it under a header that names the columns gives a BED with the same columns:

# the header names the columns, so a track or an awk filter can name repFamily
{
  printf '#genoName\tgenoStart\tgenoEnd\tname\tstrand\trepFamily\trepClass\tswScore\tmilliDiv\n'
  awk 'BEGIN { OFS = "\t" }
    # a data row is the one starting with a bare integer, its SW score
    $1 ~ /^[0-9]+$/ {
      # "LINE/L1" splits; "Simple_repeat" does not, and UCSC repeats the class
      # as the family for exactly those rows. Positions are 1-based inclusive
      # and the strand column spells minus "C".
      n = split($11, cf, "/")
      print $5, $6 - 1, $7, $10, ($9 == "C") ? "-" : "+", (n > 1) ? cf[2] : cf[1], cf[1], $1, int($2 * 10 + 0.5)
    }' repeats.out
} > rmsk.bed

# `sort-bed` is `sort -k1,1 -k2,2n` under LC_ALL=C, header kept on top
jbrowse sort-bed rmsk.bed | bgzip > rmsk.bed.gz
tabix -f -C -p bed rmsk.bed.gz

An awk filter on the repFamily column keeps the header line and the sort order, so tabix indexes the cut file as it is:

# the header line names the columns, repFamily the sixth
gzip -dc rmsk.bed.gz | awk -F'\t' -v fam=Alu '/^#/ || $6 == fam' | bgzip > Alu.bed.gz
tabix -f -C -p bed Alu.bed.gz

The track reads any BED-like file, bgzipped and CSI-indexed, with a # header line naming the columns, and a mark refers to a column by name. In grammar-of-graphics terms, encoding maps columns to a mark's channels, and color is a color scale from a field through scale.domain to scale.range. The track below lists three marks:

  • Per-copy bars (below maxBpPerPx): a bar per copy with milliDiv as the height. A formula step writes the first four characters of the name into lineage, and the ordinal scale.domain fixes the legend order
  • Copies per bin (past minBpPerPx): every Alu copy counted per bin, in grey
  • AluY per bin: the same count behind a filter for AluY, in red

Goes in the tracks array of config.json. See Tracks.

{
  "type": "FeatureTrack",
  "trackId": "alu_age",
  "name": "Alu copies",
  "assemblyNames": ["hg38"],
  "adapter": {
    "type": "BedTabixAdapter",
    "uri": "https://jbrowse.org/demos/gene_density/Alu.bed.gz",
    "csi": true
  },
  "displays": [
    {
      "type": "LinearMarkDisplay",
      "marks": [
        {
          "mark": "bar",
          "transform": [
            {
              "type": "formula",
              "expr": "jexl:substring(feature.name, 0, 4)",
              "as": "lineage"
            }
          ],
          "encoding": {
            "y": "milliDiv",
            "color": {
              "field": "lineage",
              "scale": {
                "type": "ordinal",
                "domain": ["AluJ", "AluS", "AluY", "FLAM", "FRAM"],
                "range": ["#4575b4", "#fdae61", "#d73027", "#8c8c8c", "#8c8c8c"]
              },
              "legend": { "title": "Alu lineage" }
            }
          },
          "maxBpPerPx": 100
        },
        {
          "mark": "bar",
          "transform": [
            { "type": "bin", "step": "auto" },
            {
              "type": "aggregate",
              "groupby": ["start", "end"],
              "ops": [{ "op": "count" }]
            }
          ],
          "encoding": { "color": { "value": "#c0c0c0" } },
          "minBpPerPx": 100
        },
        {
          "mark": "bar",
          "transform": [
            {
              "type": "filter",
              "expr": "jexl:startsWith(feature.name, 'AluY')"
            },
            { "type": "bin", "step": "auto" },
            {
              "type": "aggregate",
              "groupby": ["start", "end"],
              "ops": [{ "op": "count" }]
            }
          ],
          "encoding": { "color": { "value": "#d73027" } },
          "minBpPerPx": 100
        }
      ]
    }
  ]
}

Edits config.json in the current folder. See JBrowse CLI with Desktop.

jbrowse add-track-json '{
  "type": "FeatureTrack",
  "trackId": "alu_age",
  "name": "Alu copies",
  "assemblyNames": ["hg38"],
  "adapter": {
    "type": "BedTabixAdapter",
    "uri": "https://jbrowse.org/demos/gene_density/Alu.bed.gz",
    "csi": true
  },
  "displays": [
    {
      "type": "LinearMarkDisplay",
      "marks": [
        {
          "mark": "bar",
          "transform": [
            {
              "type": "formula",
              "expr": "jexl:substring(feature.name, 0, 4)",
              "as": "lineage"
            }
          ],
          "encoding": {
            "y": "milliDiv",
            "color": {
              "field": "lineage",
              "scale": {
                "type": "ordinal",
                "domain": ["AluJ", "AluS", "AluY", "FLAM", "FRAM"],
                "range": ["#4575b4", "#fdae61", "#d73027", "#8c8c8c", "#8c8c8c"]
              },
              "legend": { "title": "Alu lineage" }
            }
          },
          "maxBpPerPx": 100
        },
        {
          "mark": "bar",
          "transform": [
            { "type": "bin", "step": "auto" },
            {
              "type": "aggregate",
              "groupby": ["start", "end"],
              "ops": [{ "op": "count" }]
            }
          ],
          "encoding": { "color": { "value": "#c0c0c0" } },
          "minBpPerPx": 100
        },
        {
          "mark": "bar",
          "transform": [
            {
              "type": "filter",
              "expr": "jexl:startsWith(feature.name, '\''AluY'\'')"
            },
            { "type": "bin", "step": "auto" },
            {
              "type": "aggregate",
              "groupby": ["start", "end"],
              "ops": [{ "op": "count" }]
            }
          ],
          "encoding": { "color": { "value": "#d73027" } },
          "minBpPerPx": 100
        }
      ]
    }
  ]
}'

In JBrowse Desktop, or in any running JBrowse Web session, open a view on this track’s assembly, then File → Open track..., choose Add track from pasted JSON, and paste:

{
  "type": "FeatureTrack",
  "trackId": "alu_age",
  "name": "Alu copies",
  "assemblyNames": ["hg38"],
  "adapter": {
    "type": "BedTabixAdapter",
    "uri": "https://jbrowse.org/demos/gene_density/Alu.bed.gz",
    "csi": true
  },
  "displays": [
    {
      "type": "LinearMarkDisplay",
      "marks": [
        {
          "mark": "bar",
          "transform": [
            {
              "type": "formula",
              "expr": "jexl:substring(feature.name, 0, 4)",
              "as": "lineage"
            }
          ],
          "encoding": {
            "y": "milliDiv",
            "color": {
              "field": "lineage",
              "scale": {
                "type": "ordinal",
                "domain": ["AluJ", "AluS", "AluY", "FLAM", "FRAM"],
                "range": ["#4575b4", "#fdae61", "#d73027", "#8c8c8c", "#8c8c8c"]
              },
              "legend": { "title": "Alu lineage" }
            }
          },
          "maxBpPerPx": 100
        },
        {
          "mark": "bar",
          "transform": [
            { "type": "bin", "step": "auto" },
            {
              "type": "aggregate",
              "groupby": ["start", "end"],
              "ops": [{ "op": "count" }]
            }
          ],
          "encoding": { "color": { "value": "#c0c0c0" } },
          "minBpPerPx": 100
        },
        {
          "mark": "bar",
          "transform": [
            {
              "type": "filter",
              "expr": "jexl:startsWith(feature.name, 'AluY')"
            },
            { "type": "bin", "step": "auto" },
            {
              "type": "aggregate",
              "groupby": ["start", "end"],
              "ops": [{ "op": "count" }]
            }
          ],
          "encoding": { "color": { "value": "#d73027" } },
          "minBpPerPx": 100
        }
      ]
    }
  ]
}

Open this track in JBrowse Web ↗

This view in a notebook, with jbrowse-anywidget. Swap a track's uri for your file.

from jbrowse_anywidget import JBrowseApp, fetch_hub

config = fetch_hub("https://jbrowse.org/ucsc/hg38/config.json")
app = JBrowseApp(
    assemblies=config["assemblies"],
    tracks=config.get("tracks", []) + [
        {
            "type": "FeatureTrack",
            "trackId": "alu_age",
            "name": "Alu copies",
            "assemblyNames": [
                "hg38"
            ],
            "adapter": {
                "type": "BedTabixAdapter",
                "uri": "https://jbrowse.org/demos/gene_density/Alu.bed.gz",
                "csi": True
            },
            "displays": [
                {
                    "type": "LinearMarkDisplay",
                    "marks": [
                        {
                            "mark": "bar",
                            "transform": [
                                {
                                    "type": "formula",
                                    "expr": "jexl:substring(feature.name, 0, 4)",
                                    "as": "lineage"
                                }
                            ],
                            "encoding": {
                                "y": "milliDiv",
                                "color": {
                                    "field": "lineage",
                                    "scale": {
                                        "type": "ordinal",
                                        "domain": [
                                            "AluJ",
                                            "AluS",
                                            "AluY",
                                            "FLAM",
                                            "FRAM"
                                        ],
                                        "range": [
                                            "#4575b4",
                                            "#fdae61",
                                            "#d73027",
                                            "#8c8c8c",
                                            "#8c8c8c"
                                        ]
                                    },
                                    "legend": {
                                        "title": "Alu lineage"
                                    }
                                }
                            },
                            "maxBpPerPx": 100
                        },
                        {
                            "mark": "bar",
                            "transform": [
                                {
                                    "type": "bin",
                                    "step": "auto"
                                },
                                {
                                    "type": "aggregate",
                                    "groupby": [
                                        "start",
                                        "end"
                                    ],
                                    "ops": [
                                        {
                                            "op": "count"
                                        }
                                    ]
                                }
                            ],
                            "encoding": {
                                "color": {
                                    "value": "#c0c0c0"
                                }
                            },
                            "minBpPerPx": 100
                        },
                        {
                            "mark": "bar",
                            "transform": [
                                {
                                    "type": "filter",
                                    "expr": "jexl:startsWith(feature.name, 'AluY')"
                                },
                                {
                                    "type": "bin",
                                    "step": "auto"
                                },
                                {
                                    "type": "aggregate",
                                    "groupby": [
                                        "start",
                                        "end"
                                    ],
                                    "ops": [
                                        {
                                            "op": "count"
                                        }
                                    ]
                                }
                            ],
                            "encoding": {
                                "color": {
                                    "value": "#d73027"
                                }
                            },
                            "minBpPerPx": 100
                        }
                    ]
                }
            ]
        }
    ],
    views=[
        {
            "type": "LinearGenomeView",
            "assembly": "hg38",
            "loc": "chr1:151,000,000-151,030,000",
            "tracks": [
                "alu_age"
            ]
        }
    ],
)
app  # display the widget

This view in your React 19 app, with @jbrowse/react-app2 and @jbrowse/core. Add your own files to tracks.

import { use } from 'react'
import { JBrowse } from '@jbrowse/react-app2'
import '@jbrowse/react-app2/styles.css'
import { addRelativeUris } from '@jbrowse/core/util/addRelativeUris'

const configUrl = "https://jbrowse.org/ucsc/hg38/config.json"
const configPromise = fetch(configUrl)
  .then(res => res.json())
  .then(config => {
    addRelativeUris(config, new URL(configUrl))
    return config
  })

export default function Figure() {
  const config = use(configPromise)
  return (
    <JBrowse
      assemblies={config.assemblies}
      tracks={[...(config.tracks ?? []), ...[
          {
            "type": "FeatureTrack",
            "trackId": "alu_age",
            "name": "Alu copies",
            "assemblyNames": [
              "hg38"
            ],
            "adapter": {
              "type": "BedTabixAdapter",
              "uri": "https://jbrowse.org/demos/gene_density/Alu.bed.gz",
              "csi": true
            },
            "displays": [
              {
                "type": "LinearMarkDisplay",
                "marks": [
                  {
                    "mark": "bar",
                    "transform": [
                      {
                        "type": "formula",
                        "expr": "jexl:substring(feature.name, 0, 4)",
                        "as": "lineage"
                      }
                    ],
                    "encoding": {
                      "y": "milliDiv",
                      "color": {
                        "field": "lineage",
                        "scale": {
                          "type": "ordinal",
                          "domain": [
                            "AluJ",
                            "AluS",
                            "AluY",
                            "FLAM",
                            "FRAM"
                          ],
                          "range": [
                            "#4575b4",
                            "#fdae61",
                            "#d73027",
                            "#8c8c8c",
                            "#8c8c8c"
                          ]
                        },
                        "legend": {
                          "title": "Alu lineage"
                        }
                      }
                    },
                    "maxBpPerPx": 100
                  },
                  {
                    "mark": "bar",
                    "transform": [
                      {
                        "type": "bin",
                        "step": "auto"
                      },
                      {
                        "type": "aggregate",
                        "groupby": [
                          "start",
                          "end"
                        ],
                        "ops": [
                          {
                            "op": "count"
                          }
                        ]
                      }
                    ],
                    "encoding": {
                      "color": {
                        "value": "#c0c0c0"
                      }
                    },
                    "minBpPerPx": 100
                  },
                  {
                    "mark": "bar",
                    "transform": [
                      {
                        "type": "filter",
                        "expr": "jexl:startsWith(feature.name, 'AluY')"
                      },
                      {
                        "type": "bin",
                        "step": "auto"
                      },
                      {
                        "type": "aggregate",
                        "groupby": [
                          "start",
                          "end"
                        ],
                        "ops": [
                          {
                            "op": "count"
                          }
                        ]
                      }
                    ],
                    "encoding": {
                      "color": {
                        "value": "#d73027"
                      }
                    },
                    "minBpPerPx": 100
                  }
                ]
              }
            ]
          }
        ]]}
      aggregateTextSearchAdapters={config.aggregateTextSearchAdapters}
      configuration={config.configuration}
      views={[
        {
          "type": "LinearGenomeView",
          "assembly": "hg38",
          "loc": "chr1:151,000,000-151,030,000",
          "tracks": [
            "alu_age"
          ]
        }
      ]}
    />
  )
}

jbrowse-img draws this view as an SVG, no browser needed. Swap --config or a track for your own.

cat > tracks.json <<'JSON'
[
  {
    "type": "FeatureTrack",
    "trackId": "alu_age",
    "name": "Alu copies",
    "assemblyNames": [
      "hg38"
    ],
    "adapter": {
      "type": "BedTabixAdapter",
      "uri": "https://jbrowse.org/demos/gene_density/Alu.bed.gz",
      "csi": true
    },
    "displays": [
      {
        "type": "LinearMarkDisplay",
        "marks": [
          {
            "mark": "bar",
            "transform": [
              {
                "type": "formula",
                "expr": "jexl:substring(feature.name, 0, 4)",
                "as": "lineage"
              }
            ],
            "encoding": {
              "y": "milliDiv",
              "color": {
                "field": "lineage",
                "scale": {
                  "type": "ordinal",
                  "domain": [
                    "AluJ",
                    "AluS",
                    "AluY",
                    "FLAM",
                    "FRAM"
                  ],
                  "range": [
                    "#4575b4",
                    "#fdae61",
                    "#d73027",
                    "#8c8c8c",
                    "#8c8c8c"
                  ]
                },
                "legend": {
                  "title": "Alu lineage"
                }
              }
            },
            "maxBpPerPx": 100
          },
          {
            "mark": "bar",
            "transform": [
              {
                "type": "bin",
                "step": "auto"
              },
              {
                "type": "aggregate",
                "groupby": [
                  "start",
                  "end"
                ],
                "ops": [
                  {
                    "op": "count"
                  }
                ]
              }
            ],
            "encoding": {
              "color": {
                "value": "#c0c0c0"
              }
            },
            "minBpPerPx": 100
          },
          {
            "mark": "bar",
            "transform": [
              {
                "type": "filter",
                "expr": "jexl:startsWith(feature.name, 'AluY')"
              },
              {
                "type": "bin",
                "step": "auto"
              },
              {
                "type": "aggregate",
                "groupby": [
                  "start",
                  "end"
                ],
                "ops": [
                  {
                    "op": "count"
                  }
                ]
              }
            ],
            "encoding": {
              "color": {
                "value": "#d73027"
              }
            },
            "minBpPerPx": 100
          }
        ]
      }
    ]
  }
]
JSON

npx @jbrowse/img --config https://jbrowse.org/ucsc/hg38/config.json \
  --trackConfigs tracks.json \
  --assembly hg38 --loc chr1:151,000,000-151,030,000 \
  --track alu_age \
  --out figure.svg

For a PNG, --out figure.png (needs rsvg-convert: apt install librsvg2-bin, brew install librsvg).

Open chr1:151,000,000-151,030,000, 30 kb of 1q21, and click a bar to open its row of the BED.

Alu copies over 1q21: bar height is divergence from consensus, color is lineage.
Open in JBrowse Web ↗

Or rebuild it from your own data:

Quickest: open the view, then File → Open track... for your files.

From scratch:

  1. Open your genome: Open your own genome in JBrowse Desktop, or jbrowse add-assembly for JBrowse Web.This figure uses hg38, loaded from a .2bit genome.
  2. Add your track: File → Open track..., or check it in the track selector. Needs a bgzip-compressed, tabix-indexed BED (.bed.gz + .tbi).This figure uses “Alu copies”.
  3. Go to your region in the location box.This figure is at chr1:151,000,000-151,030,000.

Paste into a coding agent, with your goal on the first line.

My goal: [write yours, e.g. this view of my own files, or these track settings in my config.json]

Start from this JBrowse view.
- Config it loads: https://jbrowse.org/code/jb2/main/test_data/alu_age/config.json
- Tracks:
  - Alu copies (alu_age), FeatureTrack, a bgzip-compressed, tabix-indexed BED (.bed.gz + .tbi), drawn as LinearMarkDisplay

Docs: https://jbrowse.org/jb2/docs/agents_authoring/ (writing a config), https://jbrowse.org/jb2/docs/agents/ (driving a running JBrowse). Use the jbrowse-authoring, jbrowse-hosted-data and jbrowse-capture skills if you have them. Check any config with `npx @jbrowse/cli validate`, then render it and look: a config that loads is not yet a track that drew.

The session spec that draws the view:
{
  "views": [
    {
      "type": "LinearGenomeView",
      "assembly": "hg38",
      "loc": "chr1:151,000,000-151,030,000",
      "tracks": [
        {
          "trackId": "alu_age",
          "height": 200
        }
      ]
    }
  ]
}
Redraw the figure headlessly
cat > session.json <<'JSON'
{
  "views": [
    {
      "type": "LinearGenomeView",
      "assembly": "hg38",
      "loc": "chr1:151,000,000-151,030,000",
      "tracks": [
        {
          "trackId": "alu_age",
          "height": 200
        }
      ]
    }
  ]
}
JSON

cat > callouts.json <<'JSON'
[
  {
    "type": "text",
    "text": "Bar height: divergence from consensus. Older copies are taller",
    "fontSize": 18,
    "maxWidth": 400,
    "anchor": {
      "trackId": "alu_age",
      "loc": "chr1:151,010,600",
      "fracY": 0.05
    }
  }
]
JSON

npx @jbrowse/capture --instance https://jbrowse.org/code/jb2/main/ \
  --config https://jbrowse.org/code/jb2/main/test_data/alu_age/config.json \
  --width 1500 --height 410 \
  --timeout 90000 \
  --spec session.json --annotations callouts.json -o figure.png

More: Using JBrowse with AI agents.

Adds these tracks to your config.json, styled as in the figure. Point each uri at your file (replace YOUR_FILE).

jbrowse add-track-json '{
  "type": "FeatureTrack",
  "trackId": "alu_age",
  "name": "Alu copies",
  "assemblyNames": [
    "hg38"
  ],
  "adapter": {
    "type": "BedTabixAdapter",
    "uri": "YOUR_FILE"
  },
  "displayDefaults": {
    "height": 200
  }
}'

Run beside config.json, or add --out <dir>. Needs hg38 in the config (jbrowse add-assembly).

This view in a notebook, with jbrowse-anywidget. Swap a track's uri for your file.

from jbrowse_anywidget import JBrowseApp, fetch_hub

config = fetch_hub("https://jbrowse.org/code/jb2/main/test_data/alu_age/config.json")
app = JBrowseApp(
    assemblies=config["assemblies"],
    tracks=config.get("tracks", []),
    views=[
        {
            "type": "LinearGenomeView",
            "assembly": "hg38",
            "loc": "chr1:151,000,000-151,030,000",
            "tracks": [
                {
                    "trackId": "alu_age",
                    "height": 200
                }
            ]
        }
    ],
)
app  # display the widget

This view in your React 19 app, with @jbrowse/react-app2 and @jbrowse/core. Add your own files to tracks.

import { use } from 'react'
import { JBrowse } from '@jbrowse/react-app2'
import '@jbrowse/react-app2/styles.css'
import { addRelativeUris } from '@jbrowse/core/util/addRelativeUris'

const configUrl = "https://jbrowse.org/code/jb2/main/test_data/alu_age/config.json"
const configPromise = fetch(configUrl)
  .then(res => res.json())
  .then(config => {
    addRelativeUris(config, new URL(configUrl))
    return config
  })

export default function Figure() {
  const config = use(configPromise)
  return (
    <JBrowse
      assemblies={config.assemblies}
      tracks={config.tracks}
      aggregateTextSearchAdapters={config.aggregateTextSearchAdapters}
      configuration={config.configuration}
      views={[
        {
          "type": "LinearGenomeView",
          "assembly": "hg38",
          "loc": "chr1:151,000,000-151,030,000",
          "tracks": [
            {
              "trackId": "alu_age",
              "height": 200
            }
          ]
        }
      ]}
    />
  )
}

jbrowse-img draws this view as an SVG, no browser needed. Swap --config or a track for your own.

npx @jbrowse/img --config https://jbrowse.org/code/jb2/main/test_data/alu_age/config.json \
  --assembly hg38 --loc chr1:151,000,000-151,030,000 \
  --track alu_age '{"height":200}' \
  --width 1500 --out figure.svg

For a PNG, --out figure.png (needs rsvg-convert: apt install librsvg2-bin, brew install librsvg).

The session spec behind the figure, over this config.

{
  "views": [
    {
      "type": "LinearGenomeView",
      "assembly": "hg38",
      "loc": "chr1:151,000,000-151,030,000",
      "tracks": [
        {
          "trackId": "alu_age",
          "height": 200
        }
      ]
    }
  ]
}

Counting Alu copies per bin when zoomed out

Zoomed out past minBpPerPx, the track switches to the two binned marks. On a whole chromosome it exceeds its fetch budget and shows a "region too large" message, so a bigWig of copies per kilobase, counted once from the BED, covers that width:

# writes Alu.bed.density.bw beside the input, in 1 kb bins
# --chrom-sizes takes a two-column name and length table;
#   --assembly genome.fa reads the lengths off the FASTA's .fai instead
jbrowse make-density Alu.bed.gz --chrom-sizes hg38.chrom.sizes

Add the bigWig as a track:

Goes in the tracks array of config.json. See Tracks.

{
  "trackId": "alu_per_kb",
  "name": "Alu copies per kb",
  "assemblyNames": ["hg38"],
  "uri": "https://jbrowse.org/demos/gene_density/Alu.bed.density.bw",
  "displayDefaults": { "mark": { "extent": "none" } }
}

Edits config.json in the current folder. See JBrowse CLI with Desktop.

jbrowse add-track https://jbrowse.org/demos/gene_density/Alu.bed.density.bw \
  --trackId alu_per_kb \
  --name "Alu copies per kb" \
  --assemblyNames hg38 \
  --displayDefaults '{"mark":{"extent":"none"}}'

In JBrowse Desktop, or in any running JBrowse Web session, open a view on this track’s assembly, then File → Open track..., choose Add track from pasted JSON, and paste:

{
  "trackId": "alu_per_kb",
  "name": "Alu copies per kb",
  "assemblyNames": ["hg38"],
  "uri": "https://jbrowse.org/demos/gene_density/Alu.bed.density.bw",
  "displayDefaults": { "mark": { "extent": "none" } }
}

Open this track in JBrowse Web ↗

This view in a notebook, with jbrowse-anywidget. Swap a track's uri for your file.

from jbrowse_anywidget import JBrowseApp, fetch_hub

config = fetch_hub("https://jbrowse.org/ucsc/hg38/config.json")
app = JBrowseApp(
    assemblies=config["assemblies"],
    tracks=config.get("tracks", []) + [
        {
            "trackId": "alu_per_kb",
            "name": "Alu copies per kb",
            "assemblyNames": [
                "hg38"
            ],
            "uri": "https://jbrowse.org/demos/gene_density/Alu.bed.density.bw",
            "displayDefaults": {
                "mark": {
                    "extent": "none"
                }
            }
        }
    ],
    views=[
        {
            "type": "LinearGenomeView",
            "assembly": "hg38",
            "loc": "chr1",
            "tracks": [
                "alu_per_kb"
            ]
        }
    ],
)
app  # display the widget

This view in your React 19 app, with @jbrowse/react-app2 and @jbrowse/core. Add your own files to tracks.

import { use } from 'react'
import { JBrowse } from '@jbrowse/react-app2'
import '@jbrowse/react-app2/styles.css'
import { addRelativeUris } from '@jbrowse/core/util/addRelativeUris'

const configUrl = "https://jbrowse.org/ucsc/hg38/config.json"
const configPromise = fetch(configUrl)
  .then(res => res.json())
  .then(config => {
    addRelativeUris(config, new URL(configUrl))
    return config
  })

export default function Figure() {
  const config = use(configPromise)
  return (
    <JBrowse
      assemblies={config.assemblies}
      tracks={[...(config.tracks ?? []), ...[
          {
            "trackId": "alu_per_kb",
            "name": "Alu copies per kb",
            "assemblyNames": [
              "hg38"
            ],
            "uri": "https://jbrowse.org/demos/gene_density/Alu.bed.density.bw",
            "displayDefaults": {
              "mark": {
                "extent": "none"
              }
            }
          }
        ]]}
      aggregateTextSearchAdapters={config.aggregateTextSearchAdapters}
      configuration={config.configuration}
      views={[
        {
          "type": "LinearGenomeView",
          "assembly": "hg38",
          "loc": "chr1",
          "tracks": [
            "alu_per_kb"
          ]
        }
      ]}
    />
  )
}

jbrowse-img draws this view as an SVG, no browser needed. Swap --config or a track for your own.

cat > tracks.json <<'JSON'
[
  {
    "trackId": "alu_per_kb",
    "name": "Alu copies per kb",
    "assemblyNames": [
      "hg38"
    ],
    "uri": "https://jbrowse.org/demos/gene_density/Alu.bed.density.bw",
    "displayDefaults": {
      "mark": {
        "extent": "none"
      }
    }
  }
]
JSON

npx @jbrowse/img --config https://jbrowse.org/ucsc/hg38/config.json \
  --trackConfigs tracks.json \
  --assembly hg38 --loc chr1 \
  --track alu_per_kb \
  --out figure.svg

For a PNG, --out figure.png (needs rsvg-convert: apt install librsvg2-bin, brew install librsvg).

AluY share per megabase, against the genome-wide share

The red AluY count is too small to read against a total that varies between bins. A script instead writes a BED with two log2 columns: the AluY share per megabase against the genome-wide share, and the plus-strand share against one half as a control that should show no pattern.

Fetch the script:

curl -fO https://raw.githubusercontent.com/GMOD/jbrowse-components/main/scripts/alu_young_share.py
# columns: copies, young, plus, youngShare, youngLog2, strandLog2, one row per
# 1 Mb bin holding at least 50 copies; also prints the Spearman rank correlation
# of each share against copies per bin
python3 alu_young_share.py Alu.bed.gz Alu.young_share.bed AluY
bgzip -f Alu.young_share.bed
tabix -f -C -p bed Alu.young_share.bed.gz

Advanced → Edit plot... in the track menu applies edits to the cut, colors and key names live. The config below sets them in the track:

Goes in the tracks array of config.json. See Tracks.

{
  "type": "FeatureTrack",
  "trackId": "alu_young_share",
  "name": "AluY share per Mb, against the genome",
  "uri": "https://jbrowse.org/code/jb2/main/test_data/alu_age/Alu.young_share.bed.gz",
  "csi": true,
  "assemblyNames": ["hg38"],
  "displays": [
    {
      "type": "LinearMarkDisplay",
      "encoding": {
        "y": {
          "scale": { "domainMin": -1.5, "domainMax": 1.5 },
          "axis": { "title": "AluY share, log2" }
        }
      },
      "marks": [
        {
          "mark": "bar",
          "encoding": {
            "y": "youngLog2",
            "color": {
              "field": "youngLog2",
              "scale": {
                "type": "threshold",
                "domain": [0],
                "range": ["#4575b4", "#d73027"],
                "names": ["below the genome-wide share", "above it"]
              },
              "legend": { "title": "AluY share" }
            }
          }
        }
      ]
    }
  ]
}

Edits config.json in the current folder. See JBrowse CLI with Desktop.

jbrowse add-track-json '{
  "type": "FeatureTrack",
  "trackId": "alu_young_share",
  "name": "AluY share per Mb, against the genome",
  "uri": "https://jbrowse.org/code/jb2/main/test_data/alu_age/Alu.young_share.bed.gz",
  "csi": true,
  "assemblyNames": ["hg38"],
  "displays": [
    {
      "type": "LinearMarkDisplay",
      "encoding": {
        "y": {
          "scale": { "domainMin": -1.5, "domainMax": 1.5 },
          "axis": { "title": "AluY share, log2" }
        }
      },
      "marks": [
        {
          "mark": "bar",
          "encoding": {
            "y": "youngLog2",
            "color": {
              "field": "youngLog2",
              "scale": {
                "type": "threshold",
                "domain": [0],
                "range": ["#4575b4", "#d73027"],
                "names": ["below the genome-wide share", "above it"]
              },
              "legend": { "title": "AluY share" }
            }
          }
        }
      ]
    }
  ]
}'

In JBrowse Desktop, or in any running JBrowse Web session, open a view on this track’s assembly, then File → Open track..., choose Add track from pasted JSON, and paste:

{
  "type": "FeatureTrack",
  "trackId": "alu_young_share",
  "name": "AluY share per Mb, against the genome",
  "uri": "https://jbrowse.org/code/jb2/main/test_data/alu_age/Alu.young_share.bed.gz",
  "csi": true,
  "assemblyNames": ["hg38"],
  "displays": [
    {
      "type": "LinearMarkDisplay",
      "encoding": {
        "y": {
          "scale": { "domainMin": -1.5, "domainMax": 1.5 },
          "axis": { "title": "AluY share, log2" }
        }
      },
      "marks": [
        {
          "mark": "bar",
          "encoding": {
            "y": "youngLog2",
            "color": {
              "field": "youngLog2",
              "scale": {
                "type": "threshold",
                "domain": [0],
                "range": ["#4575b4", "#d73027"],
                "names": ["below the genome-wide share", "above it"]
              },
              "legend": { "title": "AluY share" }
            }
          }
        }
      ]
    }
  ]
}
Top: chromosome 1, Alu copies per kilobase above the AluY share per megabase. Below: the copies track over the same AluY share, copies per bin in grey and AluY in red.
Open in JBrowse Web ↗

Or rebuild it from your own data:

Quickest: open the view, then File → Open track... for your files.

From scratch:

  1. Open your genome: Open your own genome in JBrowse Desktop, or jbrowse add-assembly for JBrowse Web.This figure uses hg38, loaded from a .2bit genome.
  2. Add your track: File → Open track..., or check it in the track selector. Needs a BigWig file (.bw).This figure uses “Alu copies per kb”.
  3. Add the next track the same way. Needs a bgzip-compressed, tabix-indexed BED (.bed.gz + .tbi).This figure uses “AluY share per Mb, against the genome”.
  4. Go to your region in the location box.This figure is at chr1.

Rebuilds the figure headlessly. Edit the session file (location, track settings, your own track under sessionTracks) and rerun.

The figure stacks 2 frames: one command draws each, and ImageMagick stacks them.

Frame 1: Chromosome 1

cat > session-1.json <<'JSON'
{
  "views": [
    {
      "type": "LinearGenomeView",
      "assembly": "hg38",
      "loc": "chr1",
      "tracks": [
        {
          "trackId": "alu_per_kb",
          "height": 110
        },
        {
          "trackId": "alu_young_share",
          "height": 90
        }
      ]
    }
  ]
}
JSON

npx @jbrowse/capture --instance https://jbrowse.org/code/jb2/main/ \
  --config https://jbrowse.org/code/jb2/main/test_data/alu_age/config.json \
  --width 1500 --height 465 \
  --timeout 90000 \
  --spec session-1.json -o frame-1.png

Frame 2: The stretch under the wedge

cat > session-2.json <<'JSON'
{
  "views": [
    {
      "type": "LinearGenomeView",
      "assembly": "hg38",
      "loc": "chr1:184000001-212000000",
      "tracks": [
        {
          "trackId": "alu_age",
          "height": 110
        },
        {
          "trackId": "alu_young_share",
          "height": 90
        }
      ]
    }
  ]
}
JSON

cat > callouts-2.json <<'JSON'
[
  {
    "type": "text",
    "text": "Alu sparse: young share high",
    "fontSize": 18,
    "leader": true,
    "anchor": {
      "trackId": "alu_young_share",
      "loc": "chr1:191,500,000",
      "fracY": 0.3
    },
    "dx": -40,
    "dy": -95
  },
  {
    "type": "text",
    "text": "Alu dense: young share low",
    "fontSize": 18,
    "leader": true,
    "anchor": {
      "trackId": "alu_young_share",
      "loc": "chr1:203,500,000",
      "fracY": 0.75
    },
    "dx": 80,
    "dy": -177
  }
]
JSON

npx @jbrowse/capture --instance https://jbrowse.org/code/jb2/main/ \
  --config https://jbrowse.org/code/jb2/main/test_data/alu_age/config.json \
  --width 1500 --height 465 \
  --timeout 90000 \
  --spec session-2.json --annotations callouts-2.json -o frame-2.png
magick frame-1.png frame-2.png -background white -smush 70 figure.png

The figure's callouts across its frames are drawn over the stacked image, which these commands leave out.

More: Using JBrowse with AI agents.

Adds these tracks to your config.json, styled as in the figure. Point each uri at your file (replace YOUR_FILE).

jbrowse add-track-json '{
  "type": "QuantitativeTrack",
  "trackId": "alu_per_kb",
  "name": "Alu copies per kb",
  "assemblyNames": [
    "hg38"
  ],
  "adapter": {
    "type": "BigWigAdapter",
    "uri": "YOUR_FILE"
  },
  "displayDefaults": {
    "height": 110
  }
}'

jbrowse add-track-json '{
  "type": "FeatureTrack",
  "trackId": "alu_young_share",
  "name": "AluY share per Mb, against the genome",
  "assemblyNames": [
    "hg38"
  ],
  "adapter": {
    "type": "BedTabixAdapter",
    "uri": "YOUR_FILE"
  },
  "displayDefaults": {
    "height": 90
  }
}'

Run beside config.json, or add --out <dir>. Needs hg38 in the config (jbrowse add-assembly).

This view in a notebook, with jbrowse-anywidget. Swap a track's uri for your file.

from jbrowse_anywidget import JBrowseApp, fetch_hub

config = fetch_hub("https://jbrowse.org/code/jb2/main/test_data/alu_age/config.json")
app = JBrowseApp(
    assemblies=config["assemblies"],
    tracks=config.get("tracks", []),
    views=[
        {
            "type": "LinearGenomeView",
            "assembly": "hg38",
            "loc": "chr1",
            "tracks": [
                {
                    "trackId": "alu_per_kb",
                    "height": 110
                },
                {
                    "trackId": "alu_young_share",
                    "height": 90
                }
            ]
        }
    ],
)
app  # display the widget

This view in your React 19 app, with @jbrowse/react-app2 and @jbrowse/core. Add your own files to tracks.

import { use } from 'react'
import { JBrowse } from '@jbrowse/react-app2'
import '@jbrowse/react-app2/styles.css'
import { addRelativeUris } from '@jbrowse/core/util/addRelativeUris'

const configUrl = "https://jbrowse.org/code/jb2/main/test_data/alu_age/config.json"
const configPromise = fetch(configUrl)
  .then(res => res.json())
  .then(config => {
    addRelativeUris(config, new URL(configUrl))
    return config
  })

export default function Figure() {
  const config = use(configPromise)
  return (
    <JBrowse
      assemblies={config.assemblies}
      tracks={config.tracks}
      aggregateTextSearchAdapters={config.aggregateTextSearchAdapters}
      configuration={config.configuration}
      views={[
        {
          "type": "LinearGenomeView",
          "assembly": "hg38",
          "loc": "chr1",
          "tracks": [
            {
              "trackId": "alu_per_kb",
              "height": 110
            },
            {
              "trackId": "alu_young_share",
              "height": 90
            }
          ]
        }
      ]}
    />
  )
}

jbrowse-img draws this view as an SVG, no browser needed. Swap --config or a track for your own.

npx @jbrowse/img --config https://jbrowse.org/code/jb2/main/test_data/alu_age/config.json \
  --assembly hg38 --loc chr1 \
  --track alu_per_kb '{"height":110}' \
  --track alu_young_share '{"height":90}' \
  --width 1500 --out figure.svg

For a PNG, --out figure.png (needs rsvg-convert: apt install librsvg2-bin, brew install librsvg).

The session spec behind the figure, over this config.

{
  "views": [
    {
      "type": "LinearGenomeView",
      "assembly": "hg38",
      "loc": "chr1",
      "tracks": [
        {
          "trackId": "alu_per_kb",
          "height": 110
        },
        {
          "trackId": "alu_young_share",
          "height": 90
        }
      ]
    }
  ]
}
Open in JBrowse Web ↗

Or rebuild it from your own data:

Quickest: open the view, then File → Open track... for your files.

From scratch:

  1. Open your genome: Open your own genome in JBrowse Desktop, or jbrowse add-assembly for JBrowse Web.This figure uses hg38, loaded from a .2bit genome.
  2. Add your track: File → Open track..., or check it in the track selector. Needs a bgzip-compressed, tabix-indexed BED (.bed.gz + .tbi).This figure uses “Alu copies”.
  3. Add the next track the same way. Needs a bgzip-compressed, tabix-indexed BED (.bed.gz + .tbi).This figure uses “AluY share per Mb, against the genome”.
  4. Go to your region in the location box.This figure is at chr1:184000001-212000000.

Rebuilds the figure headlessly. Edit the session file (location, track settings, your own track under sessionTracks) and rerun.

The figure stacks 2 frames: one command draws each, and ImageMagick stacks them.

Frame 1: Chromosome 1

cat > session-1.json <<'JSON'
{
  "views": [
    {
      "type": "LinearGenomeView",
      "assembly": "hg38",
      "loc": "chr1",
      "tracks": [
        {
          "trackId": "alu_per_kb",
          "height": 110
        },
        {
          "trackId": "alu_young_share",
          "height": 90
        }
      ]
    }
  ]
}
JSON

npx @jbrowse/capture --instance https://jbrowse.org/code/jb2/main/ \
  --config https://jbrowse.org/code/jb2/main/test_data/alu_age/config.json \
  --width 1500 --height 465 \
  --timeout 90000 \
  --spec session-1.json -o frame-1.png

Frame 2: The stretch under the wedge

cat > session-2.json <<'JSON'
{
  "views": [
    {
      "type": "LinearGenomeView",
      "assembly": "hg38",
      "loc": "chr1:184000001-212000000",
      "tracks": [
        {
          "trackId": "alu_age",
          "height": 110
        },
        {
          "trackId": "alu_young_share",
          "height": 90
        }
      ]
    }
  ]
}
JSON

cat > callouts-2.json <<'JSON'
[
  {
    "type": "text",
    "text": "Alu sparse: young share high",
    "fontSize": 18,
    "leader": true,
    "anchor": {
      "trackId": "alu_young_share",
      "loc": "chr1:191,500,000",
      "fracY": 0.3
    },
    "dx": -40,
    "dy": -95
  },
  {
    "type": "text",
    "text": "Alu dense: young share low",
    "fontSize": 18,
    "leader": true,
    "anchor": {
      "trackId": "alu_young_share",
      "loc": "chr1:203,500,000",
      "fracY": 0.75
    },
    "dx": 80,
    "dy": -177
  }
]
JSON

npx @jbrowse/capture --instance https://jbrowse.org/code/jb2/main/ \
  --config https://jbrowse.org/code/jb2/main/test_data/alu_age/config.json \
  --width 1500 --height 465 \
  --timeout 90000 \
  --spec session-2.json --annotations callouts-2.json -o frame-2.png
magick frame-1.png frame-2.png -background white -smush 70 figure.png

The figure's callouts across its frames are drawn over the stacked image, which these commands leave out.

More: Using JBrowse with AI agents.

Adds these tracks to your config.json, styled as in the figure. Point each uri at your file (replace YOUR_FILE).

jbrowse add-track-json '{
  "type": "FeatureTrack",
  "trackId": "alu_age",
  "name": "Alu copies",
  "assemblyNames": [
    "hg38"
  ],
  "adapter": {
    "type": "BedTabixAdapter",
    "uri": "YOUR_FILE"
  },
  "displayDefaults": {
    "height": 110
  }
}'

jbrowse add-track-json '{
  "type": "FeatureTrack",
  "trackId": "alu_young_share",
  "name": "AluY share per Mb, against the genome",
  "assemblyNames": [
    "hg38"
  ],
  "adapter": {
    "type": "BedTabixAdapter",
    "uri": "YOUR_FILE"
  },
  "displayDefaults": {
    "height": 90
  }
}'

Run beside config.json, or add --out <dir>. Needs hg38 in the config (jbrowse add-assembly).

This view in a notebook, with jbrowse-anywidget. Swap a track's uri for your file.

from jbrowse_anywidget import JBrowseApp, fetch_hub

config = fetch_hub("https://jbrowse.org/code/jb2/main/test_data/alu_age/config.json")
app = JBrowseApp(
    assemblies=config["assemblies"],
    tracks=config.get("tracks", []),
    views=[
        {
            "type": "LinearGenomeView",
            "assembly": "hg38",
            "loc": "chr1:184000001-212000000",
            "tracks": [
                {
                    "trackId": "alu_age",
                    "height": 110
                },
                {
                    "trackId": "alu_young_share",
                    "height": 90
                }
            ]
        }
    ],
)
app  # display the widget

This view in your React 19 app, with @jbrowse/react-app2 and @jbrowse/core. Add your own files to tracks.

import { use } from 'react'
import { JBrowse } from '@jbrowse/react-app2'
import '@jbrowse/react-app2/styles.css'
import { addRelativeUris } from '@jbrowse/core/util/addRelativeUris'

const configUrl = "https://jbrowse.org/code/jb2/main/test_data/alu_age/config.json"
const configPromise = fetch(configUrl)
  .then(res => res.json())
  .then(config => {
    addRelativeUris(config, new URL(configUrl))
    return config
  })

export default function Figure() {
  const config = use(configPromise)
  return (
    <JBrowse
      assemblies={config.assemblies}
      tracks={config.tracks}
      aggregateTextSearchAdapters={config.aggregateTextSearchAdapters}
      configuration={config.configuration}
      views={[
        {
          "type": "LinearGenomeView",
          "assembly": "hg38",
          "loc": "chr1:184000001-212000000",
          "tracks": [
            {
              "trackId": "alu_age",
              "height": 110
            },
            {
              "trackId": "alu_young_share",
              "height": 90
            }
          ]
        }
      ]}
    />
  )
}

jbrowse-img draws this view as an SVG, no browser needed. Swap --config or a track for your own.

npx @jbrowse/img --config https://jbrowse.org/code/jb2/main/test_data/alu_age/config.json \
  --assembly hg38 --loc chr1:184000001-212000000 \
  --track alu_age '{"height":110}' \
  --track alu_young_share '{"height":90}' \
  --width 1500 --out figure.svg

For a PNG, --out figure.png (needs rsvg-convert: apt install librsvg2-bin, brew install librsvg).

The session spec behind the figure, over this config.

{
  "views": [
    {
      "type": "LinearGenomeView",
      "assembly": "hg38",
      "loc": "chr1:184000001-212000000",
      "tracks": [
        {
          "trackId": "alu_age",
          "height": 110
        },
        {
          "trackId": "alu_young_share",
          "height": 90
        }
      ]
    }
  ]
}

Reproduce it end to end

build_alu_age.sh runs every step above. It:

  1. fetches UCSC's hg38 RepeatMasker table and the reference lengths, or copies your own RepeatMasker BED and FASTA
  2. cuts out the Alu rows and indexes them
  3. counts the copies per kilobase into a bigWig, and per megabase into the AluY share BED
  4. writes a JBrowse with the copies, the bigWig and the share as tracks
curl -fO https://raw.githubusercontent.com/GMOD/jbrowse-components/main/scripts/build_alu_age.sh
bash build_alu_age.sh                     # builds ./alu_age_build/jbrowse2
npx --yes serve alu_age_build/jbrowse2    # then open the printed URL

By default the script builds the tracks over UCSC's table. bash build_alu_age.sh rmsk.bed.gz genome.fa uses your own RepeatMasker BED, and FAMILY and YOUNG pick another family and its youngest lineage.

See also

Citations