[Gmod-help] Databases and chromosome location searches

[Nigel Wilson]

Hi Scott,

Turning off autocomplete and removing it from the search options did not solve the problem.

Thanks,


Nigel Wilson
_________________________________________________
Bioinformatics Analyst
The Centre for Applied Genomics
The Hospital for Sick Children, MaRS Building - East Tower
T: 416.813.7032
:: 101 College St., Rm 14-701, Toronto, Ontario  M5G 1L7




-----Original Message-----
From: Scott Cain [mailto:scott at scottcain.net]
Sent: October-04-10 1:56 PM
To: Nigel Wilson
Cc: help at gmod.org; Gbrowse (E-mail)
Subject: Re: [Gmod-help] Databases and chromosome location searches

Hi Nigel,

What happens if you turn autocomplete off and remove it from the
search options list?  I'm wondering if it isn't set up properly in one
of the databases and that is leading to a problem.

Scott


On Mon, Oct 4, 2010 at 1:52 PM, Nigel Wilson <nigel.wilson at sickkids.ca> wrote:
> Hi Scott,
>
> Here is the config file as requested.
>
> Thanks,
>
>
> Nigel Wilson
> _________________________________________________
> Bioinformatics Analyst
> The Centre for Applied Genomics
> The Hospital for Sick Children, MaRS Building - East Tower
> T: 416.813.7032
> :: 101 College St., Rm 14-701, Toronto, Ontario  M5G 1L7
>
>
>
> -----Original Message-----
> From: Scott Cain [mailto:scott at scottcain.net]
> Sent: October-04-10 1:42 PM
> To: Nigel Wilson
> Cc: help at gmod.org; Gbrowse (E-mail)
> Subject: Re: [Gmod-help] Databases and chromosome location searches
>
> Hi Nigel,
>
> I suspect there is a problem with your configuration file, as this
> should work.  Can you send it?
>
> Also, I'm cc'ing this to the GBrowse mailing list, as there are many
> subscribers to that list that have faced all sorts of issues and can
> frequently help with questions like this.
>
> Scott
>
>
> On Mon, Oct 4, 2010 at 12:05 PM, Nigel Wilson <nigel.wilson at sickkids.ca> wrote:
>> Hi,
>>
>>
>>
>> I am trying to get chromosome searches, e.g: chr1:12344..7890123,  to work
>> within gbrowse2. My system is setup with 2 databases: hg18_scaffolds, and
>> hg18_annotations. In hg18_scaffolds, I loaded the chromosome definitions
>> from a gff3 file (e.g. chr1    hg18    chromosome  1   247249719   .   .
>> .   ID=chr1;Name=Chr1). In the hg18_annotations database, I loaded all the
>> annotations that I require. The gff3 files for the annotations database do
>> not contain any chromosome definitions. However when I do this, the search,
>>  chr1:12344..7890123, returns an error: the landmark named
>> chr1:12344..7890123 is not recognized. If I perform a different search, e.g.
>> a clone name from the annotations database, this search will return the
>> expected result. If I load everything (chromosome definitions, and
>> annotations) into 1 database, both searches work properly.
>>
>>
>>
>> Is there any way to keep my desired schema, that is, the 2 separate
>> databases, and have searches such as chr1:12344..7890123 work?
>>
>>
>>
>> Thanks,
>>
>>
>>
>> Nigel Wilson
>> _________________________________________________
>> Bioinformatics Analyst
>> The Centre for Applied Genomics
>>
>> The Hospital for Sick Children, MaRS Building - East Tower
>> ­­­­­­­­­­­(: 416.813.7032
>> *: 101 College St., Rm 14-701, Toronto, Ontario  M5G 1L7
>>
>>
>>
>>
>>
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>
>
>
> --
> ------------------------------------------------------------------------
> Scott Cain, Ph. D.                                   scott at scottcain dot net
> GMOD Coordinator (http://gmod.org/)                     216-392-3087
> Ontario Institute for Cancer Research
>
> This e-mail may contain confidential, personal and/or health information(information which may be subject to legal restrictions on use, retention and/or disclosure) for the sole use of the intended recipient. Any review or distribution by anyone other than the person for whom it was originally intended is strictly prohibited. If you have received this e-mail in error, please contact the sender and delete all copies.
>



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

This e-mail may contain confidential, personal and/or health information(information which may be subject to legal restrictions on use, retention and/or disclosure) for the sole use of the intended recipient. Any review or distribution by anyone other than the person for whom it was originally intended is strictly prohibited. If you have received this e-mail in error, please contact the sender and delete all copies.