[Gmod-help] Databases and chromosome location searches

[Nigel Wilson]

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
>
>
>
>
>
> ________________________________
> 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.
-------------- next part --------------
A non-text attachment was scrubbed...
Name: hg18.conf
Type: application/octet-stream
Size: 4253 bytes
Desc: hg18.conf
URL: <http://brie4.cshl.edu/pipermail/gmod-help/attachments/20101004/4a1030fb/attachment.obj>