Track types
Every track has a type, such as bigwig or hic, that tells the browser how to read the file and how to draw it. Genie uses two renderers:
- Project workspace and shared views use the vendored eg3 engine (the third-generation WashU Epigenome Browser). This is where you work day to day.
- The public landing browser (static web deployments only) uses Genie's own native renderer, which draws a smaller set of types.
Type names are not case-sensitive; geneAnnotation and geneannotation are the same type.
Types the workspace renders
The eg3 engine in the project workspace renders 32 track types plus one alias. The alias rgbpeak is the older WashU name for a bigBed whose features carry their own colours, and Genie maps it to bigbedcolor.
The descriptions below are general. How each type is drawn, and which display options it accepts, is decided by the eg3 engine.
Reference and annotation
| Type | What it shows | Typical source |
|---|---|---|
ruler | Coordinate ruler | none (built in) |
geneannotation | Gene and transcript models (for example refGene, GENCODE, MANE) | the browser's gene-annotation service |
refbed | Gene and transcript models from your own file | tabix-indexed refBed text file |
repeatmasker | RepeatMasker repeat annotation, coloured by repeat class | bigBed |
rmskv2 | RepeatMasker annotation in a newer file layout | bigBed |
snp | Known SNPs in view (hg19 and hg38 only) | Ensembl REST service |
jaspar | Transcription factor binding motif predictions (JASPAR) | bigBed |
omeroidr | Microscopy images linked to genes, from the Image Data Resource | image service |
Intervals
| Type | What it shows | Typical source |
|---|---|---|
bed | Genomic intervals (peaks, regions) | tabix-indexed BED |
bedcolor | Intervals with per-feature colours | tabix-indexed BED |
bigbed | Genomic intervals | bigBed |
bigbedcolor | Intervals with per-feature colours (itemRgb) | bigBed |
rgbpeak | Alias of bigbedcolor | bigBed |
categorical | Intervals coloured by category, such as chromatin states | tabix-indexed BED-like file |
qbed | Point features with a quantitative value, such as insertion counts | tabix-indexed qBED |
vcf | Sequence variants | tabix-indexed VCF |
bam | Aligned sequencing reads | BAM with .bai index |
Numerical signal
| Type | What it shows | Typical source |
|---|---|---|
bigwig | Signal (for example ChIP-seq fold change or coverage) | bigWig |
bedgraph | Signal | tabix-indexed bedGraph |
dbedgraph | Several values per interval, played as an animation | tabix-indexed text file |
boxplot | Signal summarised as box plots per bin | bigWig |
dynseq | Reference sequence with letters scaled by a signal | bigWig |
methylc | DNA methylation levels per cytosine | tabix-indexed MethylC file |
modbed | Base modification calls (for example long-read methylation) | tabix-indexed modBED |
Interactions and alignments
| Type | What it shows | Typical source |
|---|---|---|
hic | Hi-C contact matrix | .hic file |
biginteract | Pairwise interactions between loci | bigInteract (bigBed) |
longrange | Pairwise interactions between loci | tabix-indexed text file |
genomealign | Alignment between this genome and a query genome (needs Query genome) | tabix-indexed genomealign file |
Composite and animated
These types group other tracks (their child tracks are listed inside the track definition).
| Type | What it shows |
|---|---|
matplot | Several numerical tracks overlaid as lines in one panel |
dynamic | Several numerical tracks played as an animation |
dynamichic | Several Hi-C matrices played as an animation |
dynamiclongrange | Several long-range interaction tracks played as an animation |
dynamicbed | Several interval tracks played as an animation |
Types offered in the Remote Tracks dialog
The Track type list in the Remote Tracks dialog shows 31 of these: every type above except bigbedcolor and the rgbpeak alias. Tracks of type rgbpeak that come from public data hubs are mapped to bigbedcolor automatically.
Types the workspace does not render
The WashU track format list includes 13 more types that the eg3 engine in the workspace does not render:
cool, longrangecolor, hammock, g3d, pairwise, snv, snv2, protein, omero4dn, bigchain, brgfa, ballc, graph
Tracks of these types can still be in a project, for example after loading a public hub that contains them. They are kept in the project's track list (and in the Track Manager) but are not drawn. Instead, a notice above the tracks lists them:
2 tracks not rendered by this engine: <track name>, <track name>
Remove them in the Track Manager if you do not need them. Genie does not map longrangecolor onto longrange, because the two file layouts differ and the result would be drawn wrongly.
Native renderer (public landing browser)
The public landing browser at / and /browser/hg19 uses Genie's native SVG renderer, not eg3. It shows the default tracks for hg38 and hg19 and its container draws these types:
ruler, geneannotation, refbed, bigwig, bedgraph, bigbed, bed, categorical, qbed, repeatmasker, rmskv2
Default heights in the native renderer:
| Track | Default height |
|---|---|
| Ruler | 40 px |
| bigWig, bedGraph | 40 px |
| bigBed, BED, categorical, qBED | 60 px |
RepeatMasker (including rmskv2) | 40 px |
| Gene annotation, refBed | grows with the number of rows (14 px per row, up to 50 rows) |
Types outside this list are not drawn by the native renderer.
Default colours in the native renderer:
| Element | Colour |
|---|---|
| Gene models | #0000FF (blue) |
| bigBed features, forward strand | #0000FF |
| bigBed features, reverse strand | #FF0000 |
| bigWig positive values | #0000FF |
| bigWig negative values | #FF8C00 |
| Gene categories (when a track colours by category) | coding #6501A8, non-coding #01C14B, pseudogene #E600AC, problem #E00202, polyA #ED7F02, other #808080 |
| RepeatMasker classes (examples) | SINE #CC0000, LINE #FF6600, LTR #006600, DNA #4A72E8 |
In the project workspace, Genie sets the categoryColors option of the gencodeV47 default track to a GENCODE palette (coding #003CB3, non-coding #008000, pseudogene #E600AC, problem #FF0000, polyA #000033) unless the track's options already set categoryColors.
The native renderer also has a larger type registry used by the developer pages and the IGVF bundle. That registry is described for developers in Browser engine.