Re: [Gmod-ajax] next generation sequencing visualization

[Ian H. <ih...@be...>]

Mitch just added Sequence Tracks (which could be hacked to show 
alignments) and also plans to allow arbitrary text in features at 
base-resolution.

However, in order to load this many features you would need some work, 
hence my comments about incremental loading of NCLists.

Steve Taylor wrote:
> Hi Ian,
> 
>> PS as Jason Stajich just remarked to me, you can already generate a 
>> WIG track representing read depth at any given site.
> 
> Yes...but we really need a decent alignment viewer at the bp level to 
> see SNPs etc. Can GBrowse display alignments in the panel?
> 
> The closest I have seen on the web is LookSeq.
> 
> http://www.sanger.ac.uk/Software/analysis/lookseq/
> 
>>
>> Ian Holmes wrote:
>>> It has come up.... obviously this is very important.
>>>
>>> One approach would be to use this as the first test case for a plugin 
>>> image track (c.f. GBrowse glyphs).
> 
> Are you thinking of using existing GBrowse routines for this to generate 
> tiles (pre-rendered or on on the fly) like in the old Ajax GBrowse?
> 
> Steve
> 
>>>
>>> Another approach is to use this to motivate piecewise loading of 
>>> feature-rich tracks, and do layout (& rendering) on the client.
>>>
>>> Both are in tune with what we eventually want to do...
>>>
>>> As always, do please let us know if you're able to contribute to 
>>> either of these (the first, server-side approach is probably the most 
>>> easily addressed by non-core developers)
>>>
>>> I.
>>>
>>>
>>> Steve Taylor wrote:
>>>> Hi,
>>>>
>>>> Is anyone looking at a way of visualizing alignments from next 
>>>> generation sequencing in JBrowse?
>>>>
>>>> Kind regards and thanks,
>>>>
>>>> Steve
>>>> ------------------------------------------------------------------
>>>> Medical Sciences Division
>>>> Weatherall Institute of Molecular Medicine/Sir William Dunn School
>>>> Oxford University
>>>>
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