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

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

On 09/29/2009 06:44 AM, Shankar Ajay Subramanian wrote:
> I circumvented the problem by converting my data to a log scale (base
> 2), so the track looks like a set of jagged peaks that I expected to
> see.
>    

Did the log scale solve the problem for you?  In other words, does the 
log display convey all of the relevant variation, or is there some 
variation that you'd like to see but can't?

> The use case that you described (100 vs 200 and 100k vs 200k) both
> constitute interesting differences since there is a two-fold
> difference between the min and max for the two regions.

Can there be 100-200 variation and also 100k-200k variation within the 
same region?  If so, are both of those still interesting?

Or do large fluctuations tend to happen only between widely separated areas?

>   In my
> particular case, if I were to compare two conditions/experiments (say,
> pre- and post-treatment) where a particular region varies between
> 1-500 (which is no doubt "interesting"), I'm unable to see this
> difference on the browser currently, since the threshold to have a
> data point displayed with my data range (1-200k) is ~1000. I suppose
> vertical scaling will help fix this. Correct me if I am wrong.
>    

I think it should help, yes.

> I don't know if I answered your question, but I'd be happy to answer
> any further questions that you might have in making improvements.
>    

You did answer my questions, thanks.  Once we get to implementing the 
log scaling and vertical scale bar and vertical zooming in JBrowse, it 
would be helpful to get feedback on how well those things work for you.

Thanks,
Mitch