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

[Shankar A. S. <sha...@gm...>]

On Tue, Sep 29, 2009 at 9:02 AM, Mitch Skinner
<mit...@be...> wrote:
> 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?

It seems to be working well so far. I have to yet compare it with
another track. Will let you know if I run into some trouble.

>
>> 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?
>

I think I'll have to answer this rather circuitously. If that were to
were, it would definitely be interesting. It's tough to say if both
those variations in one region is something one might see. Sorry, if
the answer sounds silly.

>>  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.

Definitely, I presume you'll post a message to list informing us on upgrades.

>
> Thanks,
> Mitch
>