[Gmod-help] Re: [Gmod-gbrowse] wiggle tracks in gbrowse

[Nina Thiessen]

Hi Dave,
Thank you for your suggestions.
I am not totally sure what the conf file is (I certainly do not provide 
the file), but I suspect that that is what I can modify when I click on 
the "?" associated with my track -- what I see is these settings:
[001]
glyph       = wiggle_xyplot
key         = TEST_chr_LG_XIII
description = TEST_chr_LG_XIII
pos_color=red
neg_color=blue
height  = 40

reference=LG_XIII
001 LG_XIII.data 118980..119605 
Name=TEST_chr_LG_XIII;Note=TEST_chr_LG_XIII;wigfile=/var/www/gbrowse/tmp/Poptr1.1/uploaded_file/cf3a76bda0f9b059c80427ffcc63df8d/track_001.LG_XIII.1237246714.wig

Unfortunately, inserting autoscale=global or autoscale=local into the 
above config did not change the display at all.
Please let me know if you have any other ideas.

regards,
Nina

Dave Clements, GMOD Help Desk wrote:
> Hi Nina,
>
> As I read the documentation, setting viewLimits should do the trick.
> What does the stanza for this track look like in the GBrowse
> configuation file?  Have you tried setting autoscale = global in the
> conf file?  Although, it sounds like the global max is being
> incorrectly set, so maybe try autoscale = local instead.
>
> Dave C.
>
> Was this helpful?  Let us know at http://gmod.org/wiki/Help_Desk_Feedback
>
>
>
> On Mon, Mar 16, 2009 at 5:08 PM, Nina Thiessen <nthiessen at bcgsc.ca> wrote:
>   
>> greetings,
>> (I tried looking through the archives for this mailing list, but could
>> not find the answer to my question....probably because I was just not
>> using the correct keywords or something because I can't believe I'm the
>> first person to have encountered this....)
>>
>> I am trying to view "peaks" data encoded in a fixed-step, step size=1
>> wig formatted file using a version of gbrowse on this website
>> http://www.popgenie.db.umu.se/popgenie/index.php
>> and have encountered a most vexing problem.
>>
>> I have found that no matter what I do, the maximum obtained value in the
>> series of values associated with the first fixedStep determines the max
>> display height, and so any data above that height in subsequent peaks
>> appears truncated. (I am viewing the data in "full" mode so the peaks
>> will look like bar charts) Note that the first peak in the file can be
>> well outside the region I am currently viewing and the truncation will
>> still occur.
>>
>> Setting the viewLimits in the track line does not affect anything.
>> Including the span=1 in the fixedStep line does not change anything.
>> If I change the elements to variableStep format instead of using
>> fixedStep, this does not change anything
>>
>> I confirmed there was nothing wrong with the format of the file by
>> changing the chromosome name in my test file to a more standard name
>> (chr2), and was able to load my test file into the ucsc genome browser
>> (and the display height problem does not happen there.)
>>
>> Any ideas how I can get this to work right?
>>
>> --- File format details ---
>> ("track" to "40:40:2" is all one line)
>> eg:
>> track type="wiggle_0" name="TEST_chr_LG_XIII"
>> description="TEST_chr_LG_XIII" color=50,50,150 yLineMark=0.0
>> yLineOnOff=on visibility=full priority=1 maxHeightPixels=40:40:2
>> fixedStep chrom=LG_XIII start=119600 step=1
>> 1
>> 1
>> 2
>> 3
>> 3
>> 5
>> 4
>> 2
>> 2
>> 1
>> fixedStep chrom=LG_XIII start=119653 step=1
>> 1
>> 1
>> 2
>> 3
>> 5
>> 10
>> 15
>> 20
>> 17
>> 10
>> 8
>> 5
>> 3
>> 2
>> 1
>>
>> (in the this example, the second peak will be truncated to be 5 units tall)
>>
>> regards,
>> Nina
>>
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