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Provided Genome Tracks¶

GenomeSpy provides three tracks, that are intended to be used with genomic data. To add any of these tracks to your view specification, use the import directive.

Genome axis track¶

Name: genomeAxis

Genome axis track displays the chromosome boundaries, names, and intra-chromosomal coordinates.

Cytoband track¶

Name: cytobands

Cytoband track displays the cytobands if the genome configuration provides them.

Gene annotations¶

Name: geneAnnotation

Gene track displays RefSeq gene annotations. As it is impractical to show all 20 000 gene symbols at the same time, gene track uses score-based prioritization to display only the most popular genes of the currently visible region. For profound discussion on the popularity metric, read more in "The most popular genes in the human genome" in Nature.

To save some precious screen estate, the isoforms of the genes in the provided annotation are unioned. Thus, each gene is displayed as a single "super isoform" (there are a few exceptions, though).

Hovering the gene symbols with the mouse pointer fetches gene summary information from RefSeq and displays it in a tooltip. Clicking the right mouse button on a gene symbol opens a context-menu that provides shortcuts to certain databases for further information about the gene.

How the scoring is actually done

Follow https://docs.higlass.io/data_preparation.html#gene-annotation-tracks
Use utils/compressGeneAnnotations.py to compress the geneAnnotations.bed file.
Save the file as refSeq_genes_scored_compressed.GENOME_NAME.txt and place it in the genome directory.

Example¶

This example displays cytobands, gene annotations, and genomic coordinates using the hg38 genome assembly. It also imports a COSMIC Cancer Gene Census track from genomespy.app website.

{
  "genome": { "name": "hg38" },
  "concat": [
    { "import": { "name": "cytobands" } },
    { "import": { "name": "geneAnnotation" } },
    {
      "import": {
        "url": "https://genomespy.app/tracks/cosmic/census_hg38.json"
      }
    },
    { "import": { "name": "genomeAxis" } }
  ]
}