Link between CycleDash and UCSC Genome Browser

[ihodes]

[danvk]

@arahuja @timodonnell @ryan-williams is this something you guys want? What would you want it to link to, exactly? The standard collection of tracks for hg19 at each particular locus?

[arahuja]

I haven't really used UCSC so I don't have any strong feelings on this.

[timodonnell]

UCSC's has a huge number of possible tracks, and supports loading tracks directly from third party servers using their "track hubs" (examples).

My understanding, though I'm not 100% sure, is that UCSC can only load BAMs and other data that are accessible publicly over HTTP or FTP, since the UCSC server originates the request, not the client. I don't think UCSC is going to let me look at my BAM stored on demeter without us exposing the http server publicly (which we probably don't want to do, although perhaps UCSC supports some kind of HTTP auth, not sure), or running a local instance of the UCSC server.

Since I'm not going to be able to look at my BAM in UCSC, the utility of linking directly to UCSC is pretty limited.

Perhaps ideally what we'd want is a way for CycleDash to show any annotation track that UCSC can show. I don't have any immediate use case in mind for this beyond dbSNP and COSMIC though, which it sounds like CycleDash may support soon anyway.

[danvk]

It would be useful if you wanted to learn more about a specific locus on the genome using information unrelated to the specific run, e.g. determining if it's highly conserved across mammals, if it's linked to cancer, etc.