[Genome] Browser Feature Suggestion: augmented 'move' control to support move-by-feature

[Ann Zweig]

Hello again, Malcolm,

	That's curious that you can't make the next/previous item feature work 
properly.  Here are a few things to try.

1. Turn it on by pressing the 'configure' button then checking the 
"Next/previous item navigation" check-box and hitting submit.

2. In the genome browser, be sure to turn on a gene track such as Known Genes. 
You must display the track at a visibility of full or pack.

3. Make sure you have a gene within the browser image.  You can try this 
location to see the GABRA3 gene:  chrX:151,125,422-151,159,563.  At this 
zoom-level you will see two exons in the display.  There are three more exons to 
the left of the display and six more to the right.  You can access those exons 
(bring them into view) by clicking on the double-headed open arrows at the 
respective edge of the gene.  If you hold your mouse over the double-headed open 
arrows you will see the number of exons "off the screen".

	If you are still unable to view the feature, please reply to me off-list and I 
can help you troubleshoot.


Regards,

----------
Ann Zweig
UCSC Genome Bioinformatics Group
http://genome.ucsc.edu



Cook, Malcolm wrote:
> Ann,
> 
> Spot on, I'd forgotten about that tip... I think the reason why is that
> I could never make it work....
> 
> Sorry to be obtuse but I've enabled it and don't see any difference....
> 
> Nor do I see documentation at
> http://genome.ucsc.edu/goldenPath/help/hgTracksHelp.html#FineTuning
> 
> What am I missing?
> 
> (Firefox 1.5 - javascript & java & popups enabled)
> 
> Malcolm Cook
> Database Applications Manager - Bioinformatics
> Stowers Institute for Medical Research - Kansas City, Missouri
>   
> 
>> -----Original Message-----
>> From: Ann Zweig [mailto:ann at soe.ucsc.edu] 
>> Sent: Wednesday, October 25, 2006 12:56 PM
>> To: Cook, Malcolm
>> Cc: genome at soe.ucsc.edu
>> Subject: Re: [Genome] Browser Feature Suggestion: augmented 
>> 'move' control to support move-by-feature
>>
>> Hello Malcolm,
>>
>> 	Thanks for the suggestion.  We will consider 
>> implementing it, or something like 
>> it, in the future.  In the mean time, I wonder if you have found our 
>> "next/previous item navigation" feature.  This feature allows 
>> you to navigate to 
>> the next (or previous) exon or other item of interest in each 
>> track.    It 
>> advances the track to the right or left bringing into view 
>> the next item in that 
>> track.  I know that this isn't exactly what you're looking 
>> for, but it's not too 
>> far off.  I envision your feature request acting something 
>> like this, but moving 
>> the entire next item(s) into the view.
>>
>> 	To enable this feature, press the 'configure' button 
>> from the genome browser 
>> page.  Then check the "Next/previous item navigation" 
>> check-box and hit submit.
>>
>>
>> Regards,
>>
>> ----------
>> Ann Zweig
>> UCSC Genome Bioinformatics Group
>> http://genome.ucsc.edu
>>
>>
>>
>> Cook, Malcolm wrote:
>>> Hi,
>>>
>>> Background: the genome browser's existing 'move' controls 
>> operate at the
>>> unit of the 'vertical gridline'
>>> (http://genome.ucsc.edu/goldenPath/help/hgTracksHelp.html#NAV).
>>>
>>> Feature Suggestions: augment the 'move' control to  support 
>> moving at
>>> the unit of the displayed feature (of a user-selected type).  
>>>
>>> Use case: the user could then easily tweak the display to 
>> broaden/narrow
>>> it on the left of right side so as to usefully include, for 
>> example, N
>>> more/fewer genes, BAC End Pairs, mRNAs, etc.
>>>
>>> I would not expect this capability to be applicable to 
>> tracks computed
>>> on-the-fly (Restr Enzymes) or wiggle tracks (GC percent).
>>>
>>> Any chance?
>>>
>>> And, of course....
>>>
>>> ...Thanks for the great tool
>>>
>>> Cheers,
>>>
>>> Malcolm Cook
>>> Database Applications Manager - Bioinformatics
>>> Stowers Institute for Medical Research - Kansas City, Missouri
>>>  
>>>
>>> _______________________________________________
>>> Genome maillist  -  Genome at soe.ucsc.edu
>>> http://www.soe.ucsc.edu/mailman/listinfo/genome