Support Sashimi Plot

[sehilyi]

Resources:

• MISO: https://miso.readthedocs.io/en/fastmiso/sashimi.html#why-is-it-called-sashimi-plot
• IGV: http://software.broadinstitute.org/software/igv/Sashimi
• ggsashimi: https://github.com/guigolab/ggsashimi/blob/master/ggsashimi.py
  • https://jbrowse.org/code/jb2/v1.5.1/?session=local-ncGnIgOgs
• Different Representation: https://github.com/jmw86069/splicejam
• https://github.com/isihya/long_read_isoform_visualizer
• Annotation Tool: https://github.com/griffithlab/regtools
• JBrowse: https://github.com/elsiklab/sashimiplot

[sehilyi]

The splice junctions can be inferred by using both a BAM file and a BED/GFF file.

However, Gosling does not allow combining multiple datasets in a single track. Given that we load BAM data using worker for the performance, we allow users to feed a BED/GFF file to the BAM data fetcher so that the junction annotation can be inferred directly from the BAM worker:

{
   type: 'bam',
   url: '...',
   indexUrl: '...',
   splice: { annotationUrl: '...' } // when specified, we infer junctions with coverage
}

[sehilyi]

To-Do

• [ ] Ignore skipped ranges (N) when calculating coverages
• [ ] Coverage calculation directly from the BAM worker
• [ ] A way to flip some of arcs