Cancer genome demo - Githubissues

cmdcolin commented 4 years ago

We should make a cancer genome demo

This would maybe involve

Nice display of structural variants
CNV display
Maybe the linked-supplementary reads display, I think this is very powerful and was proposed on a recent poster so should probably land
Translocation/breakpoint split view
Long read vs ref or cancer contig vs ref (the cancer assembled contig could be annotated with genes showing a duplication or similar which would be very powerful)
Spreadsheet with features in it
If the circos view could display a feature track along the ring that would be cool and then our demo wouldn't require showing just translocations
Maybe display STAR fusion as a linear track
Maybe display FusionInspector contigs https://github.com/FusionInspector/FusionInspector/wiki

We already have many SKBR3 long read datasets, but these above examples are possible next steps

cmdcolin commented 4 years ago

We should refer to the literature and show example regions from published figures or tables of SVs

cmdcolin commented 4 years ago

Example CYTH1-EIF3H fusion demonstrated in ribbon paper, supposedly found in other literature www biorxiv org_content_10 1101_082123v1 full pdf

I am not sure exactly how this will look in our view but we can try to load it

GMOD / jbrowse-components