Re: [Gmod-ajax] JBrowse wiggle file display - png

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

The short answer is; right now you can set the scale with the --min and 
--max command line parameters.

Sometime soon, we'll be implementing a log scale option.  Enabling the 
user to zoom vertically is something I'd like to do; there's a basic 
version of that that would be easy to implement (toggling between a 
"full" and "compressed" vertical axis is what I have in mind).  Would 
any of those things help in your case?

Implementing a vertical scale indicator is definitely on the to-do list.

Brenton Gravely has been advocating making the vertical scale adjust to 
the values in the visible region; I think that would be hard to 
implement so it's probably not going to happen near-term unless someone 
wants to tackle it.

I only have a basic understanding of exactly what people are using 
RNA-seq for.  So I'd like to know: in your case, how does the data 
answer a biological question?  If (say) one region has variation between 
100 and 200, and another region has variation between 100,000 and 
200,000, are the 100-200 differences and the 100k-200k differences both 
interesting?  In other words, what constitutes meaningful variation your 
RNA-seq data?

I keep asking these questions, and so far I haven't gotten an answer 
that has made it clear for me.  Maybe we're at an exploratory stage 
where the answers aren't clear in general?  I don't know.  It's tough to 
make good UI decisions if the use case isn't clear.

Mitch

On 09/28/2009 01:24 PM, Shankar Ajay Subramanian wrote:
> Hi,
>
> I'm a newbie to JBrowse and I was wondering if someone could help me
> out with my question. I currently have a de novo genome assembly on
> which I'd like to overlay wiggle tracks from RNA-seq data. The wiggle
> file (variableStep) has values that are in the range 1-275000. This
> (huge) range of values is probably why most of the regions appear to
> be without any reads/expression - the low values are probably not
> rendered in the png image.
>
> I'm wondering if there's a solution to see the data at a better
> resolution/scale. Are there options while converting to json that I
> can use to make it appear better? Is dynamic scaling possible as a
> user zooms in/out? Or should I do my own scaling/transposition before
> I do the json conversion?
>
> Thanks,
> Shankar
>
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