Structural variants from Hi-C

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.13. Desktop beta builds are coming soon.

Two chromosomes joined by a translocation touch along the join, so Hi-C reads linking them run far above background. We look for the Philadelphia chromosome, the BCR-ABL1 fusion, in the Hi-C of the K562 leukemia line against GM12878's normal karyotype. JBrowse fetches a Hi-C matrix for every pair of regions on screen, so a chr9 window and a chr22 window in one linear view draw the contacts between the two. Over the same matrices, we then compare the two lines' compartment calls at EBF1, a gene B cells depend on for their identity.

Prerequisites

a JBrowse to paste the tracks into (Web or Desktop)
java, which juicer_tools needs for the scan script; the script downloads juicer_tools itself
curl, for the same scan script

Where the data comes from

Deep in situ Hi-C for GM12878 and K562 from ENCODE, plus ENCODE's domain, loop and compartment calls over the same two matrices.

Nothing to download: the track configs and the scan script below read these files by URL.

The files

GM12878 in situ Hi-C (ENCSR410MDC): https://encode-public.s3.amazonaws.com/2021/10/28/6f0cc163-86c7-4a68-baac-65af90f5a90d/ENCFF053VBX.hic
K562 in situ Hi-C (ENCSR545YBD): https://encode-public.s3.amazonaws.com/2021/10/28/4d332729-3463-4782-b33c-76e4fa8ff72a/ENCFF080DPJ.hic
GM12878 contact domains (Arrowhead): https://encode-public.s3.amazonaws.com/2021/10/28/467750ae-7aab-47b0-a304-dc5f8dff89f7/ENCFF301CUL.bedpe.gz
GM12878 loops (HiCCUPS): https://encode-public.s3.amazonaws.com/2021/10/28/70e6944c-1212-45f9-855c-dbc74e9a21f5/ENCFF712NKX.bedpe.gz
GM12878 compartment eigenvector: https://encode-public.s3.amazonaws.com/2021/10/28/5b488af0-df49-4b9b-9feb-8ad671b7eaef/ENCFF661LPK.bigWig
K562 compartment eigenvector: https://encode-public.s3.amazonaws.com/2021/10/28/1180b7b2-99fd-429a-bfe1-f76cc8aa751a/ENCFF699RSL.bigWig

Reading a Hi-C contact map: the triangle, domains and loops

Hi-C counts how often two stretches of the genome touch in the nucleus. JBrowse draws the result as a triangle: the diagonal runs along the top edge, and depth below it is genomic separation. Two features of that picture have names, and ENCODE publishes both as annotation files derived from the matrix:

Contact domains (also called topologically associating domains, TADs) are the square blocks sitting on the diagonal. Inside one, everything contacts everything; across a boundary, contact drops sharply. ENCODE calls them with Arrowhead and ships a BEDPE.
Loops are individual bright dots off the diagonal: two specific points contacting each other far more than their separation predicts, usually a pair of convergent CTCF sites. ENCODE calls them with HiCCUPS, also a BEDPE.

Over a wide window the triangle can render as red speckle. If a Hi-C track looks like noise, change resolutionBias first, which steps to coarser bins (adjusting resolution).

Loading the GRCh38 assembly

ENCODE aligned both Hi-C libraries to GRCh38, so we load that assembly before adding any track.

Config file

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"
}

CLI (add-assembly)

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"}'

JBrowse Desktop

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

In JBrowse Desktop, Open new 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

Adding the Hi-C and contact-domain tracks

The .hic files are 20 GB and 55 GB, and JBrowse requests only the bins on screen.

Config file

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

{
  "trackId": "hic_k562_insitu",
  "name": "K562 in situ Hi-C (ENCODE ENCSR545YBD)",
  "uri": "https://encode-public.s3.amazonaws.com/2021/10/28/4d332729-3463-4782-b33c-76e4fa8ff72a/ENCFF080DPJ.hic",
  "assemblyNames": ["hg38"],
  "displayDefaults": {
    "selectedNormalization": "NONE"
  }
}

CLI (add-track)

jbrowse add-track https://encode-public.s3.amazonaws.com/2021/10/28/4d332729-3463-4782-b33c-76e4fa8ff72a/ENCFF080DPJ.hic \
  --trackId hic_k562_insitu \
  --name "K562 in situ Hi-C (ENCODE ENCSR545YBD)" \
  --assemblyNames hg38 \
  --displayDefaults '{"selectedNormalization":"NONE"}'

In the app

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": "hic_k562_insitu",
  "name": "K562 in situ Hi-C (ENCODE ENCSR545YBD)",
  "uri": "https://encode-public.s3.amazonaws.com/2021/10/28/4d332729-3463-4782-b33c-76e4fa8ff72a/ENCFF080DPJ.hic",
  "assemblyNames": ["hg38"],
  "displayDefaults": {
    "selectedNormalization": "NONE"
  }
}

Config file

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

{
  "trackId": "hic_gm12878_insitu",
  "name": "GM12878 in situ Hi-C, deep (ENCODE ENCSR410MDC)",
  "uri": "https://encode-public.s3.amazonaws.com/2021/10/28/6f0cc163-86c7-4a68-baac-65af90f5a90d/ENCFF053VBX.hic",
  "assemblyNames": ["hg38"],
  "displayDefaults": {
    "selectedNormalization": "NONE"
  }
}

CLI (add-track)

jbrowse add-track https://encode-public.s3.amazonaws.com/2021/10/28/6f0cc163-86c7-4a68-baac-65af90f5a90d/ENCFF053VBX.hic \
  --trackId hic_gm12878_insitu \
  --name "GM12878 in situ Hi-C, deep (ENCODE ENCSR410MDC)" \
  --assemblyNames hg38 \
  --displayDefaults '{"selectedNormalization":"NONE"}'

In the app

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": "hic_gm12878_insitu",
  "name": "GM12878 in situ Hi-C, deep (ENCODE ENCSR410MDC)",
  "uri": "https://encode-public.s3.amazonaws.com/2021/10/28/6f0cc163-86c7-4a68-baac-65af90f5a90d/ENCFF053VBX.hic",
  "assemblyNames": ["hg38"],
  "displayDefaults": {
    "selectedNormalization": "NONE"
  }
}

Use ENCODE's direct S3 URLs. hic-straw's range reader cannot follow the cross-origin redirect the portal's @@download links return, and the .hic comes back as a 403. The S3 URL for any ENCODE file is in its metadata under cloud_metadata.url.

The domain BEDPE needs one extra slot, "type": "FeatureTrack":

Config file

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

{
  "type": "FeatureTrack",
  "trackId": "hic_gm12878_domains",
  "name": "GM12878 contact domains (Arrowhead)",
  "assemblyNames": ["hg38"],
  "adapter": {
    "type": "BedpeAdapter",
    "uri": "https://encode-public.s3.amazonaws.com/2021/10/28/467750ae-7aab-47b0-a304-dc5f8dff89f7/ENCFF301CUL.bedpe.gz"
  }
}

CLI (add-track)

jbrowse add-track https://encode-public.s3.amazonaws.com/2021/10/28/467750ae-7aab-47b0-a304-dc5f8dff89f7/ENCFF301CUL.bedpe.gz \
  --trackId hic_gm12878_domains \
  --name "GM12878 contact domains (Arrowhead)" \
  --assemblyNames hg38 \
  --trackType FeatureTrack

In the app

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": "hic_gm12878_domains",
  "name": "GM12878 contact domains (Arrowhead)",
  "assemblyNames": ["hg38"],
  "adapter": {
    "type": "BedpeAdapter",
    "uri": "https://encode-public.s3.amazonaws.com/2021/10/28/467750ae-7aab-47b0-a304-dc5f8dff89f7/ENCFF301CUL.bedpe.gz"
  }
}

Arrowhead writes each domain with both BEDPE ends set to the same interval, so as a FeatureTrack the file gives one box per domain, nested domains stacking into rows. Loops, whose mates differ, are the paired-arc case in the Hi-C track config guide; the whole GM12878 loops track is hic_gm12878_loops in https://jbrowse.org/code/jb2/main/test_data/config_demo.json.

To color or filter either track by a column, set columnNames explicitly.¹

Opening chr9 and chr22 in one view to look for the translocation

Type both locations into the location box, separated by a space: chr9:129,730,000-131,730,000 chr22:22,285,000-24,285,000.

A chr22 window entered into the location box beside a chr9 one, GM12878 above and K562 below: the wedge between the two triangles appears with the second region.

Video

Open the session the video starts in ↗, then take the steps it shows:

One chr9 window: each Hi-C track is chr9 against itself
Enter ABL1's chr9 window and BCR's chr22 one, space-separated
Between the triangles, chr9 meets chr22 in K562 only: the fusion

Steps

Open this view in JBrowse Web ↗ · Open this view in JBrowse Desktop ↗

Desktop link does nothing?

It needs JBrowse Desktop 5.0+. Or 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%22hg38%22%2C%22loc%22%3A%22chr9%3A129%2C730%2C000-131%2C730%2C000%22%2C%22trackLabels%22%3A%22offset%22%2C%22highlight%22%3A%5B%7B%22refName%22%3A%22chr9%22%2C%22start%22%3A130713881%2C%22end%22%3A130887675%2C%22label%22%3A%22ABL1%22%2C%22color%22%3A%22rgba%2830%2C110%2C190%2C0.16%29%22%7D%2C%7B%22refName%22%3A%22chr22%22%2C%22start%22%3A23180509%2C%22end%22%3A23318037%2C%22label%22%3A%22BCR%22%2C%22color%22%3A%22rgba%2830%2C110%2C190%2C0.16%29%22%7D%5D%2C%22tracks%22%3A%5B%7B%22trackId%22%3A%22mane_hg38%22%2C%22type%22%3A%22LinearBasicDisplay%22%2C%22showLabels%22%3A%22name%22%2C%22height%22%3A68%7D%2C%7B%22trackId%22%3A%22hic_gm12878_insitu%22%2C%22type%22%3A%22LinearHicDisplay%22%2C%22height%22%3A380%2C%22color%22%3A%7B%22scale%22%3A%22linear%22%7D%2C%22useColorPercentile%22%3Atrue%2C%22selectedNormalization%22%3A%22NONE%22%2C%22squashToHeight%22%3Afalse%7D%2C%7B%22trackId%22%3A%22hic_k562_insitu%22%2C%22type%22%3A%22LinearHicDisplay%22%2C%22height%22%3A380%2C%22color%22%3A%7B%22scale%22%3A%22linear%22%7D%2C%22useColorPercentile%22%3Atrue%2C%22selectedNormalization%22%3A%22NONE%22%2C%22squashToHeight%22%3Afalse%7D%5D%7D%5D%7D&sessionName=JBrowse+docs%3A+hic%2Ftwo_regions

The short route: open the view in JBrowse Web, where File → Open track... adds your own files beside its hosted genome and tracks.

From scratch with your own data, the steps behind the figure:

Open your genome: on the JBrowse Desktop start screen click Open new genome (or Show all available genomes to pick a hosted one). For JBrowse Web, jbrowse add-assembly puts it in your config.json.This figure uses hg38, loaded from a bgzip-compressed FASTA (.fa.gz + .fai + .gzi).
Add a track: check one your config has in the track selector, or File → Open track... to paste a URL or choose a local file. This one needs a BigBed file (.bb).This figure uses “MANE 1.0”.
1. Track menu → Show... → Labels → Name only
Add the next track the same way. This one needs a Hi-C file (.hic).This figure uses “GM12878 in situ Hi-C, deep (ENCODE ENCSR410MDC)”.
1. Track menu → Color scheme → Log scale (unchecked)
2. Track menu → Color scheme → Emphasize faint contacts (95th percentile) (checked)Saturates the color scale at the 95th percentile instead of the maximum, so faint off-diagonal contacts read more strongly.
3. Track menu → Normalization → NONEThe submenu lists only the schemes the file actually carries, and ticks the one the loaded matrix has rather than the one requested. NONE is raw observed counts, which is what a rearrangement needs — matrix balancing divides an amplified fusion back out.
4. Track menu → Show... → Fit to display height (unchecked)Squashes the triangle vertically to fill the track instead of drawing square bins at its natural half-the-view-width height. Unchecked keeps square bins, which fits when the feature of interest sits nearer the diagonal than the track is tall.
Add the next track the same way. This one needs a Hi-C file (.hic).This figure uses “K562 in situ Hi-C (ENCODE ENCSR545YBD)”.
1. Track menu → Color scheme → Log scale (unchecked)
2. Track menu → Color scheme → Emphasize faint contacts (95th percentile) (checked)Saturates the color scale at the 95th percentile instead of the maximum, so faint off-diagonal contacts read more strongly.
3. Track menu → Normalization → NONEThe submenu lists only the schemes the file actually carries, and ticks the one the loaded matrix has rather than the one requested. NONE is raw observed counts, which is what a rearrangement needs — matrix balancing divides an amplified fusion back out.
4. Track menu → Show... → Fit to display height (unchecked)Squashes the triangle vertically to fill the track instead of drawing square bins at its natural half-the-view-width height. Unchecked keeps square bins, which fits when the feature of interest sits nearer the diagonal than the track is tall.
Type your region of interest into the location box and press Enter.This figure is at chr9:129,730,000-131,730,000.
View menu → Show... → Offset
View menu → Zoom to region / use the location box, then add a highlightThis figure highlights 2 regions; highlights can also be set with the &highlight= URL parameter.

Spec

This session spec draws the figure. It goes after &session=spec- on a JBrowse Web link that loads https://jbrowse.org/code/jb2/main/test_data/config_demo.json, which is what the Web button above opens.

{
  "views": [
    {
      "type": "LinearGenomeView",
      "assembly": "hg38",
      "loc": "chr9:129,730,000-131,730,000",
      "trackLabels": "offset",
      "highlight": [
        {
          "refName": "chr9",
          "start": 130713881,
          "end": 130887675,
          "label": "ABL1",
          "color": "rgba(30,110,190,0.16)"
        },
        {
          "refName": "chr22",
          "start": 23180509,
          "end": 23318037,
          "label": "BCR",
          "color": "rgba(30,110,190,0.16)"
        }
      ],
      "tracks": [
        {
          "trackId": "mane_hg38",
          "type": "LinearBasicDisplay",
          "showLabels": "name",
          "height": 68
        },
        {
          "trackId": "hic_gm12878_insitu",
          "type": "LinearHicDisplay",
          "height": 380,
          "color": {
            "scale": "linear"
          },
          "useColorPercentile": true,
          "selectedNormalization": "NONE",
          "squashToHeight": false
        },
        {
          "trackId": "hic_k562_insitu",
          "type": "LinearHicDisplay",
          "height": 380,
          "color": {
            "scale": "linear"
          },
          "useColorPercentile": true,
          "selectedNormalization": "NONE",
          "squashToHeight": false
        }
      ]
    }
  ]
}

Notebook

The same view with jbrowse-anywidget, from the config the figure loads. Swap a track's uri for your own file.

from jbrowse_anywidget import JBrowseApp, fetch_hub

config = fetch_hub("https://jbrowse.org/code/jb2/main/test_data/config_demo.json")
app = JBrowseApp(
    assemblies=config["assemblies"],
    tracks=config.get("tracks", []),
    views=[
        {
            "type": "LinearGenomeView",
            "assembly": "hg38",
            "loc": "chr9:129,730,000-131,730,000",
            "trackLabels": "offset",
            "highlight": [
                {
                    "refName": "chr9",
                    "start": 130713881,
                    "end": 130887675,
                    "label": "ABL1",
                    "color": "rgba(30,110,190,0.16)"
                },
                {
                    "refName": "chr22",
                    "start": 23180509,
                    "end": 23318037,
                    "label": "BCR",
                    "color": "rgba(30,110,190,0.16)"
                }
            ],
            "tracks": [
                {
                    "trackId": "mane_hg38",
                    "type": "LinearBasicDisplay",
                    "showLabels": "name",
                    "height": 68
                },
                {
                    "trackId": "hic_gm12878_insitu",
                    "type": "LinearHicDisplay",
                    "height": 380,
                    "color": {
                        "scale": "linear"
                    },
                    "useColorPercentile": True,
                    "selectedNormalization": "NONE",
                    "squashToHeight": False
                },
                {
                    "trackId": "hic_k562_insitu",
                    "type": "LinearHicDisplay",
                    "height": 380,
                    "color": {
                        "scale": "linear"
                    },
                    "useColorPercentile": True,
                    "selectedNormalization": "NONE",
                    "squashToHeight": False
                }
            ]
        }
    ],
)
app  # display the widget

Image

jbrowse-img draws the same view as an SVG, from the command line and without a browser. Point --config at your own config, or swap a track for your own file with --bam, --vcfgz and the other file flags.

npx @jbrowse/img --config https://jbrowse.org/code/jb2/main/test_data/config_demo.json \
  --assembly hg38 --loc chr9:129,730,000-131,730,000 \
  --trackLabels offset \
  --track mane_hg38 display:LinearBasicDisplay '{"showLabels":"name","height":68}' \
  --track hic_gm12878_insitu display:LinearHicDisplay '{"height":380,"color":{"scale":"linear"},"useColorPercentile":true,"selectedNormalization":"NONE","squashToHeight":false}' \
  --track hic_k562_insitu display:LinearHicDisplay '{"height":380,"color":{"scale":"linear"},"useColorPercentile":true,"selectedNormalization":"NONE","squashToHeight":false}' \
  --width 1920 --out figure.svg

It has no flag for this figure's highlight, so its picture can differ there.

--out figure.png writes a PNG instead, through rsvg-convert (apt install librsvg2-bin, brew install librsvg).

Agent

Hand this to a coding agent. It rebuilds the figure above headlessly, and the session file is then the thing to edit: change the location or a track's settings, or add your own track under sessionTracks, and rerun.

cat > session.json <<'JSON'
{
  "views": [
    {
      "type": "LinearGenomeView",
      "assembly": "hg38",
      "loc": "chr9:129,730,000-131,730,000",
      "trackLabels": "offset",
      "highlight": [
        {
          "refName": "chr9",
          "start": 130713881,
          "end": 130887675,
          "label": "ABL1",
          "color": "rgba(30,110,190,0.16)"
        },
        {
          "refName": "chr22",
          "start": 23180509,
          "end": 23318037,
          "label": "BCR",
          "color": "rgba(30,110,190,0.16)"
        }
      ],
      "tracks": [
        {
          "trackId": "mane_hg38",
          "type": "LinearBasicDisplay",
          "showLabels": "name",
          "height": 68
        },
        {
          "trackId": "hic_gm12878_insitu",
          "type": "LinearHicDisplay",
          "height": 380,
          "color": {
            "scale": "linear"
          },
          "useColorPercentile": true,
          "selectedNormalization": "NONE",
          "squashToHeight": false
        },
        {
          "trackId": "hic_k562_insitu",
          "type": "LinearHicDisplay",
          "height": 380,
          "color": {
            "scale": "linear"
          },
          "useColorPercentile": true,
          "selectedNormalization": "NONE",
          "squashToHeight": false
        }
      ]
    }
  ]
}
JSON

npx @jbrowse/capture --instance https://jbrowse.org/code/jb2/main/ \
  --config https://jbrowse.org/code/jb2/main/test_data/config_demo.json \
  --width 1920 --height 1238 \
  --spec 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.

Two regions on separate chromosomes touch at background rate. If they are fused, they contact each other constantly.

K562 has the Philadelphia chromosome, t(9;22)(q34;q11) (Rowley 1973), joining BCR on chr22 to ABL1 on chr9.

ABL1 (chr9) and BCR (chr22) as two windows in one linear view, GM12878 above and K562 below. The wedge between the two panels' triangles is chr9 against chr22: empty in GM12878, a dense block under the arrow in K562.

The domain boundaries inside each window line up between the two lines, so chr9 and chr22 each fold normally in K562.

Choosing the control and normalization for the translocation scan

Control depth. The scan script below compares a case .hic against a control, ENCODE's deep GM12878 in situ file ENCSR410MDC by default. The script leaves the much shallower GM12878 "supernatant" fraction, ENCSR730CER, commented out, because a wedge empty for want of reads looks the same as one empty for want of a translocation. With the deep file, the scan finds GM12878 with more contact than K562 across the whole chr9-chr22 block except the junction bin, where the order inverts.

Normalization. Matrix balancing divides out per-bin coverage differences, and an amplified fusion is such a difference, so balancing hides it. Re-run the scan with NORM=INTER_SCALE and ABL1×BCR drops off the top of the table. Balanced matrices suit domains and loops and raw counts suit rearrangements, so both Hi-C tracks here set selectedNormalization to NONE.

The scan prints a ranked list for the control below the one for the case. The top bin in the control list is hot in both GM12878 and K562, so it is a reproducible mapping artifact and not a rearrangement.

Ranking chr9-chr22 contact bins with juicer_tools

Finding the translocation takes one dump per .hic file and a sort. Dump the raw contact counts between the two chromosomes:

# NONE: raw counts, for the reason above
# BP 250000: 250 kb base-pair bins
# -Xmx4g: a whole chromosome pair needs more than the default heap
java -Xmx4g -jar juicer_tools.jar dump observed NONE \
  case.hic chr9 chr22 BP 250000 case.txt

An empty output file means the .hic stores nothing at that resolution, or has no vector for the normalization you asked for (a file may store those only at coarser bins). The file has three columns: bin1 start, bin2 start and contact count. Rank the bins by count:

# awk in place of head, which would kill sort with SIGPIPE under pipefail
sort -k3,3 -rn case.txt | awk 'NR <= 10'

scan_hic_translocation.sh dumps the case and the control, ranks the case bins and prints the control count beside each:

curl -fO https://raw.githubusercontent.com/GMOD/jbrowse-components/main/scripts/scan_hic_translocation.sh
bash scan_hic_translocation.sh

Override CASE, CTRL, CHR1, CHR2, RES and NORM to scan any two .hic files that hold inter-chromosomal blocks. Reading the output:

The top row pairs ABL1 intron 1 with the 5' end of BCR.
RES=10000 lands on the junction itself, ABL1 intron 1 against the BCR major breakpoint cluster region. The K562 fusions tutorial places the DNA break of the same fusion in that intron.
A second chr9-chr22 bin further down also sits well clear of the control, so treat the ranking as a list of candidates to open.

Purpose-built callers scan the whole genome: EagleC, hic_breakfinder and HiNT. Each writes BEDPE, which loads here as a paired-arc track next to the matrix it was called from.

A and B compartments at EBF1 in GM12878 and K562

The genome sorts into two interleaved sets of regions, the gene-rich, active A compartment and the inactive B compartment, and each region contacts regions in the same set most. ENCODE publishes that call for every experiment as a compartment eigenvector and a set of subcompartment classes.

We load each line's eigenvector, a score per bin whose sign marks the compartment, as a bigWig. Both tracks pin scales.y, the y scale, to one symmetric range, so they compare directly and 0, where the compartment flips, sits in the middle of each:

Config file

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

{
  "trackId": "hic_gm12878_compartments",
  "name": "GM12878 compartment eigenvector (ENCFF661LPK)",
  "uri": "https://encode-public.s3.amazonaws.com/2021/10/28/5b488af0-df49-4b9b-9feb-8ad671b7eaef/ENCFF661LPK.bigWig",
  "assemblyNames": ["hg38"],
  "displayDefaults": {
    "scales": { "y": { "domainMin": -0.012, "domainMax": 0.012 } }
  }
}

CLI (add-track)

jbrowse add-track https://encode-public.s3.amazonaws.com/2021/10/28/5b488af0-df49-4b9b-9feb-8ad671b7eaef/ENCFF661LPK.bigWig \
  --trackId hic_gm12878_compartments \
  --name "GM12878 compartment eigenvector (ENCFF661LPK)" \
  --assemblyNames hg38 \
  --displayDefaults '{"scales":{"y":{"domainMin":-0.012,"domainMax":0.012}}}'

In the app

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": "hic_gm12878_compartments",
  "name": "GM12878 compartment eigenvector (ENCFF661LPK)",
  "uri": "https://encode-public.s3.amazonaws.com/2021/10/28/5b488af0-df49-4b9b-9feb-8ad671b7eaef/ENCFF661LPK.bigWig",
  "assemblyNames": ["hg38"],
  "displayDefaults": {
    "scales": { "y": { "domainMin": -0.012, "domainMax": 0.012 } }
  }
}

The K562 track uses https://encode-public.s3.amazonaws.com/2021/10/28/1180b7b2-99fd-429a-bfe1-f76cc8aa751a/ENCFF699RSL.bigWig. On an eigenvector track already open, Y axis... → Range writes the same two ends. Open both eigenvector tracks over EBF1 on chr5:

GM12878 and K562 eigenvector tracks over the same window: the band at EBF1 is in opposite compartments in the two lines while the frame edges agree.

The band over EBF1 is in the A compartment in GM12878, a B-lymphoblastoid line, and the B compartment in K562, an erythroleukemia, while the sequence either side of it agrees. The sign of an eigenvector is arbitrary, so use the gene track to tell which sign is A, the gene-rich compartment.

External links

HiGlass

Notes

Juicer writes a version banner after the header line, so column names read from the header come out undefined past the tenth column, and a jexl expression on one of them matches nothing and reports no error. HiCCUPS writes 24 columns and Arrowhead 16, and both leave name and score at . and put what they rank by further along: observed for HiCCUPS, a second column called score for Arrowhead. Values past the tenth column arrive as strings, so compare with > and <, which coerce. ↩

Feedback on this tutorial is welcome: contact us.

Structural variants from Hi-C

Prerequisites#

Where the data comes from#

Reading a Hi-C contact map: the triangle, domains and loops#

Loading the GRCh38 assembly#

Adding the Hi-C and contact-domain tracks#

Opening chr9 and chr22 in one view to look for the translocation#

Choosing the control and normalization for the translocation scan#

Ranking chr9-chr22 contact bins with juicer_tools#

A and B compartments at EBF1 in GM12878 and K562#

See also#

External links#

Notes

Prerequisites

Where the data comes from

Reading a Hi-C contact map: the triangle, domains and loops

Loading the GRCh38 assembly

Adding the Hi-C and contact-domain tracks

Opening chr9 and chr22 in one view to look for the translocation

Choosing the control and normalization for the translocation scan

Ranking chr9-chr22 contact bins with juicer_tools

A and B compartments at EBF1 in GM12878 and K562

See also

External links