Re: [Gmod-ajax] next generation sequencing visualization

[Mitch S. <mit...@be...>]

Steve Taylor wrote:
> In addition an alignment display would be useful for viewing 
> conservation across species at the base pair level and is already part 
> of the UCSC browser.

This part we can almost do now.  The client-side work for showing 
sequence is done, although there's currently no mechanim for 
insertions.  The client side sequence stuff was written with the ref seq 
in mind; for alignments, gaps are easy to represent, and display, but 
insertions would need more work to do something like UCSC does.

It ought to be straightforward, though.  It's the short-read stuff 
that's more of a challenge, although with the incremental feature 
loading that Ian was talking about it should be do-able, as long as the 
density of reads isn't too ungodly high.  We have to do incrememtal 
loading anyway for other kinds of dense tracks.

Actually, what is a reasonable (rough estimate) upper bound on the read 
density?  Is this something we can expect to change over time?  Also, 
does anyone have some data I could test with?

Mitch