Re: [Gmod-ajax] next generation sequencing visualization

[Steve T. <ste...@im...>]

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
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>>> Oxford University
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