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

[cwilks]

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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>
>
>
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