[Gmod-help] Re: [Gmod-gbrowse] gbrowse and the wiggle format

[Scott Cain]

Hi Chris,

It is possible for users to upload wiggle data--I'm pretty sure
MODEncode does it with their GBrowse.

Scott


On Wed, Nov 12, 2008 at 2:50 PM, cwilks <cwilks at stanford.edu> wrote:
> Hi Dave,
>
> Sorry for the time lapse, that worked (the name length was the issue),
> however, I  have another question.  Do you know if this method can be
> supported for user uploaded tracks or is it just a webserver/backend thing?
> As far as I can tell, it would seem this only works for someone reloading
> the whole gbrowse database from the server side, and that the user wouldn't
> be able to upload wiggle tracks, although we'd be interested in doing such a
> thing.
>
> Thanks for your help,
> Chris
>
>
> ----- Original Message ----- From: "Dave Clements, GMOD Help Desk"
> <gmodhelp at googlemail.com>
> To: "cwilks" <cwilks at stanford.edu>
> Cc: <gmod-gbrowse at lists.sourceforge.net>
> Sent: Tuesday, November 04, 2008 3:21 PM
> Subject: Re: [Gmod-gbrowse] gbrowse and the wiggle format
>
>
>> Hi Chris,
>>
>> I took a look at the data and configurations below and nothing stand
>> out as an obvious problem.  However, here is one thing to try:
>>
>> The Wiggle file format def at
>> http://genome.ucsc.edu/goldenPath/help/customTrack.html#TRACK says the
>> name attribute value must be 15 characters or less.  Try shortening
>> name by 1 char.
>>
>> Are any errors showing up in the apache error log?
>>
>> Thanks,
>>
>> Dave C.
>>
>>
>> On Fri, Oct 31, 2008 at 12:39 PM, cwilks <cwilks at stanford.edu> wrote:
>>>
>>>  Hi,
>>>
>>> We have a question about using gbrowse 1.69 with the wiggle format.
>>>
>>> We followed the instructions found here:
>>> http://mckay.cshl.edu/gbrowse/tutorial/tutorial.html
>>> and here:
>>> http://gmod.org/wiki/Gbrowse/Uploading_Wiggle_Tracks
>>>
>>> The track and the plot axis show up, but no data.
>>>
>>> Any help would be appreciated.
>>>
>>> Thanks,
>>> Chris Wilks
>>> TAIR
>>>
>>> Our configuration is as follows:
>>>
>>> [brg_snps]
>>> feature        = brg_snps
>>> glyph          = wiggle_xyplot
>>> graph_type     = boxes
>>> height         = 50
>>> scale          = right
>>> category       = Variation
>>> description    = 1
>>> key            = brg SNPs
>>>
>>> Our gff3 file:
>>>
>>> ##gff-version 3
>>> Chr4    .       brg_snps   1470    18578708        .       .
>>> .
>>>
>>> Name=brg%20associations;Note=snp%20associations%20in%20arabidopsis;wigfile=/tmp/track_001.Chr4.1224712771.wig
>>>
>>>
>>> We have read permissions on the binary wiggle file and it is present at
>>> that location in the file system.
>>>
>>> A sample of the format of our wiggle file:
>>>
>>> track type=wiggle_0 name="brg associations" description="snp
>>> associations in arabidopsis" color=255,255,255 altColor=0,0,0
>>> windowingFunction=mean smoothingWindow=16
>>> variableStep chrom=Chr4 span=1
>>> 1470    0.512027
>>> 1513    0.759486
>>> 1575    0.845194
>>> 1699    0.0566117
>>> 1928    0.221377
>>> 2062    0.286202
>>> 2876    0.503692
>>>
>>> -------------------------------------------------------------------------
>>> This SF.Net email is sponsored by the Moblin Your Move Developer's
>>> challenge
>>> Build the coolest Linux based applications with Moblin SDK & win great
>>> prizes
>>> Grand prize is a trip for two to an Open Source event anywhere in the
>>> world
>>> http://moblin-contest.org/redirect.php?banner_id=100&url=/
>>> _______________________________________________
>>> Gmod-gbrowse mailing list
>>> Gmod-gbrowse at lists.sourceforge.net
>>> https://lists.sourceforge.net/lists/listinfo/gmod-gbrowse
>>>
>>
>>
>>
>> --
>> Was this helpful?  Let us know at http://gmod.org/wiki/Help_Desk_Feedback
>>
>
>



-- 
------------------------------------------------------------------------
Scott Cain, Ph. D.                                   scott at scottcain dot net
GMOD Coordinator (http://gmod.org/)                     216-392-3087
Ontario Institute for Cancer Research