# Gene density and transposon density along a chromosome **TL;DR:** we look at where the genes sit along human chromosome 1 and which transposons keep them company: Alu elements pile up where the genes are, and L1 elements where they are not. A whole chromosome holds more genes, and far more repeat copies, than a browser fetches at once, so each track carries a small bigWig of feature counts per kilobase, built once with `jbrowse make-density`, that the track draws as a band wherever its features are too many to fetch and drops the moment they fit. ## Prerequisites - a JBrowse to open the figures' sessions in ([Web](https://jbrowse.org/jb2/docs/quickstart_web) or [Desktop](https://jbrowse.org/jb2/docs/quickstart_desktop)); every file here is a URL, so nothing needs hosting to read along - the [JBrowse CLI](https://jbrowse.org/jb2/docs/cli), for `jbrowse make-density` and the track it attaches to - `bedGraphToBigWig` from the [UCSC utilities](https://hgdownload.soe.ucsc.edu/admin/exe/), which `make-density` runs - htslib (`bgzip`, `tabix`), for the counts at the end - `node`, for [Reproduce it end to end](#reproduce-it-end-to-end) only ## Where the data comes from The figures read UCSC's hg38 annotation tables, rehosted on jbrowse.org with a density sidecar beside each file. - RefSeq curated genes, UCSC's `ncbiRefSeqCurated` table as GFF3: https://jbrowse.org/ucsc/hg38/ncbiRefSeqCurated.gff.gz - RepeatMasker, UCSC's `rmsk` table as BED with a column header: https://jbrowse.org/ucsc/hg38/rmsk.bed.gz - reference lengths, for the bigWig header: https://hgdownload.soe.ucsc.edu/goldenPath/hg38/bigZips/hg38.chrom.sizes - the sequence: https://hgdownload.soe.ucsc.edu/goldenPath/hg38/bigZips/hg38.2bit - the genes the figures open, with `.tbi` and `.density.bw` beside it: https://jbrowse.org/demos/gene_density/genes.gff.gz - the Alu copies cut from the RepeatMasker table, likewise: https://jbrowse.org/demos/gene_density/Alu.bed.gz - the L1 copies: https://jbrowse.org/demos/gene_density/L1.bed.gz - the simple repeats, the control: https://jbrowse.org/demos/gene_density/Simple_repeat.bed.gz ## A chromosome of genes Open the session on chromosome 1 with the four tracks. None of them fetches its features at this width: a track that would have to pull tens of thousands of records to draw a screen stops at the estimate and, since each of these has a density sidecar, draws that instead. Each band is the track's features per kilobase along the chromosome, scaled to its own peak.
The gene band and the Alu band share their peaks, the L1 band is close to their negative, and the simple-repeat band, which has no reason to follow either, does not. The gap in every band is the centromere. ## The band is a bigWig beside the file The sidecar is one bigWig per track: the number of features starting in each 1 kb bin, counted once from the file. `jbrowse make-density` reads the GFF3 and writes it beside the input, named for the file with `.density.bw` in place of its `.gz`: ```bash # --chrom-sizes gives the bigWig header its reference lengths; # --assembly hg38.fa reads them off the FASTA's .fai instead # a GFF3 counts only lines with no Parent= attribute, so a gene is one # count however many transcripts and exons hang under it; a BED, GTF # or VCF counts every record # every bin is written, empty ones included, so the bigWig's zoomed-out # levels average over the whole span rather than over the bins with a hit jbrowse make-density genes.gff.gz --chrom-sizes hg38.chrom.sizes ``` `jbrowse add-track genes.gff.gz` then finds `genes.gff.density.bw` beside the file and attaches it on its own; a sidecar elsewhere, or a remote one, is named with `--density`. What it writes is the `densityAdapter` slot on the track's adapter, a BigWigAdapter over the sidecar: ```json addtrack { "type": "FeatureTrack", "trackId": "hg38_genes", "name": "RefSeq curated genes", "assemblyNames": ["hg38"], "adapter": { "type": "Gff3TabixAdapter", "gffGzLocation": { "uri": "https://jbrowse.org/demos/gene_density/genes.gff.gz" }, "index": { "location": { "uri": "https://jbrowse.org/demos/gene_density/genes.gff.gz.tbi" } }, "densityAdapter": { "type": "BigWigAdapter", "bigWigLocation": { "uri": "https://jbrowse.org/demos/gene_density/genes.gff.density.bw" } } }, "displayDefaults": { "densityTierBpPerPx": 50000 } } ``` The slot is on the adapter rather than the display, so every display over the file gets the band. `densityTierBpPerPx` is the one display setting here, and it is optional: on the smaller chromosomes a screen of genes fits the fetch budget, and the band is the point at that zoom, so the gene track asks for it from 50 kb per pixel outward rather than leaving the swap to the budget alone. The repeat tracks need no such nudge. The three repeat tracks are the RepeatMasker table cut into one BED per family on its `repFamily` column, so that the Alu track's features are Alus and its sidecar counts Alus. The same `make-density` line over each family's BED gives its sidecar. ## Zooming in gives the features back Zoom to 10 Mb over 1q21 to 1q23. The gene track's fetch now fits, so its band is gone and the genes are drawn. The Alu and L1 tracks would still each pull thousands of records for this window, so they keep their bands.
The swap is on what a fetch would cost, not on how wide the view is: the gene track and the Alu track are the same width here and only one of them is over budget. A track with a sidecar also carries a **Density tier** entry in its track menu, with **Automatic**, **Features only** and **Density only**, so the band can be held or dropped by hand. ## Checking the band against the file The bands are counts, so the file answers the same question. Each band names its peak in its corner, and hovering it reads the sidecar's value under the cursor. Take one megabase under the tallest run of the gene band, at 155 Mb, and one under a trough, at 60 Mb, and count what falls in each. A gene's transcripts and exons carry `Parent=`, so the gene line drops them and counts each gene once: ```bash tabix genes.gff.gz chr1:155,000,000-156,000,000 | grep -vc 'Parent=' tabix Alu.bed.gz chr1:155,000,000-156,000,000 | wc -l tabix L1.bed.gz chr1:155,000,000-156,000,000 | wc -l ``` | window, chr1 | genes | Alu | L1 | simple repeats | | ------------- | ----- | ---- | --- | -------------- | | 155 to 156 Mb | 49 | 1298 | 254 | 269 | | 60 to 61 Mb | 4 | 146 | 295 | 235 | The gene count runs with the Alu count and against the L1 count, and the simple repeats come out about the same in both, which is the shape the four bands drew. ## Reproduce it end to end Every step above is wrapped in one script, [`build_gene_density.sh`](https://github.com/GMOD/jbrowse-components/blob/main/scripts/build_gene_density.sh): ```bash curl -fO https://raw.githubusercontent.com/GMOD/jbrowse-components/main/scripts/build_gene_density.sh bash build_gene_density.sh # builds ./gene_density_build/jbrowse2 npx --yes serve gene_density_build/jbrowse2 # then open the printed URL ``` It fetches the two UCSC tables and the reference lengths, cuts the RepeatMasker table into the three family BEDs, builds a sidecar for each of the four files, and writes a JBrowse with the four tracks. The tools it needs are the ones under [Prerequisites](#prerequisites). ## See also - [](https://jbrowse.org/jb2/docs/tutorials/repeatmasker_classes) - [](https://jbrowse.org/jb2/docs/cli) - [](https://jbrowse.org/jb2/docs/quickstart_web) ## References - Lander et al. (2001). [Initial sequencing and analysis of the human genome](https://doi.org/10.1038/35057062) - Smit, Hubley and Green (2013-2015). [RepeatMasker Open-4.0](https://www.repeatmasker.org)