[Gmod-gbrowse] [Gmod-help] Re: gbrowse and the wiggle format
Sheldon McKay
sheldon.mckay at gmail.com
Wed Nov 12 18:50:19 EST 2008
Hi Chris,
Some light reading...
http://gmod.org/wiki/Gbrowse/Uploading_Wiggle_Tracks
Sheldon
On Wed, Nov 12, 2008 at 4:30 PM, cwilks <cwilks at stanford.edu> wrote:
> 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
>>>>>
>>>>> -------------------------------------------------------------------------
>>>>> 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
>>
>
>
> -------------------------------------------------------------------------
> 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
>
--
Sheldon J. McKay, PhD
Research Investigator
Cold Spring Harbor Laboratory
Office: 516-367-6998
Fax: 516 367-6851
Email: mckays at cshl.edu
Skype: mckays630
More information about the Gmod-help
mailing list