Re: [Gmod-ajax] next generation sequencing visualization

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

Incidentally, in case it's not clear, I think that dealing with next-gen 
sequencing data is a **crucial** issue for JBrowse. Any pushback from us 
about high-volume feature tracks is simply about the best short-term way 
to achieve this (innovative visualization strategies, vs simply scaling 
up the idea of a clickable feature track). It is NOT meant to minimize 
the importance of next-gen sequencing data in genome browsers!


Ian Holmes wrote:
> hmmm, I think you can easily construct situations where people might 
> want to eyeball reads at the basepair level. Including insertions 
> (which, fwiw, I think can be displayed a little more easily than per 
> your email, Mitch -- e.g. as popups.)
> 
> Technically I think this comes down to a volume-of-data issue. Point 
> being that you can already visualize short reads in aggregate, by 
> generating a WIG plot of read density (easy) or by generating your own 
> image track (almost as easy).
> 
> The only thing you currently cannot do is load a genome's worth of short 
> reads into your web browser (nor would you want to do this). So, at the 
> level of core tech, this comes down to how you deal with annotation 
> tracks containing millions of features. The obvious answer being that 
> you load them incrementally (e.g. in chunks [as we currently handle 
> sequence] or by CGI range queries).
> 
> As an open source, developer-friendly project, we should be encouraging 
> people (as a first resort) to make maximal use of the APIs and parts 
> that we've already provided. That API should be extended only when it 
> simply fails to meet a significant (empirical) demand.
> 
> So I think that I'd essentially agree with what Mitch said. Consider 
> first what you can do using an image track (it might go further than you 
> think -- e.g. you could display SNPs using a sequence logo) and whether 
> it is at all possible that you could implement this yourself (obviously, 
> with help from us).
> 
> At some point we will implement partial loading extensions that will 
> allow you to eyeball high-volume feature tracks. But this will happen 
> faster if you can demonstrate that you have already pushed back to your 
> users with simpler (image-based) alternatives and they are, 
> nevertheless, in need of a high-volume solution!
> 
> BTW, Sean Eddy has a discussion thread on next-gen sequencing challenges:
> http://selab.janelia.org/people/eddys/blog/?p=86
> 
> Ian
> 
> 
> Mitch Skinner wrote:
>> Steve Taylor wrote:
>>> 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 volume of data is large, right?  So why would someone want to 
>> eyeball it?  Won't people be running programs to identify SNPs, rather 
>> than trying to do it manually?
>>
>> I worked with biologists for several years, so I know how much they like 
>> to eyeball things.  But if the data volume is large, IMHO it's important 
>> to push back and advocate automated analysis instead.  I'd hate to do a 
>> lot of work only to find that after the initial burst of enthusiasm no 
>> one used it.
>>
>> Currently, there's an assumption built fairly widely into JBrowse (and 
>> all other genome browsers as far as I know), which is that the 
>> coordinate system defined by the reference sequence doesn't change on 
>> the fly.  So it'll take a fair chunk of work to be able to show 
>> insertions from resequencing.
>>
>> On the other hand, if you're talking about viewing just a small region, 
>> and you want to view it in alignment coordinates, and all of your data 
>> is in aligment coordinates, then the JBrowse part of the work should be 
>> easy to do.  We've talked about displaying per-base data (like sequence, 
>> or a predicted RNA fold) in features; it's not implemented but it should 
>> be straightforward to do.
>>
>> Mitch
> 
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