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

[cwilks]

Ok, Thanks Scott.  I'll checkout what the MODEncode folks are doing.

Chris
----- Original Message ----- 
From: "Scott Cain" <cain.cshl at gmail.com>
To: "cwilks" <cwilks at stanford.edu>
Cc: <help at gmod.org>; <gmod-gbrowse at lists.sourceforge.net>
Sent: Wednesday, November 12, 2008 12:42 PM
Subject: Re: [Gmod-help] Re: [Gmod-gbrowse] gbrowse and the wiggle format


> 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
>>>>
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>>>
>>>
>>>
>>> --
>>> 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
>