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¶
Genome axis track displays the chromosome boundaries, names, and intra-chromosomal coordinates.
Cytoband track displays the cytobands if the genome configuration provides them.
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
utils/compressGeneAnnotations.pyto compress the
- Save the file as
refSeq_genes_scored_compressed.GENOME_NAME.txtand place it in the genome directory.
This example displays cytobands, gene annotations, and genomic coordinates
hg38 genome assembly. It also imports a COSMIC Cancer Gene
Census track from genomespy.app