[Gmod-help] Databases and chromosome location searches

[Nigel Wilson]

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.
-------------- next part --------------
An HTML attachment was scrubbed...
URL: <http://brie4.cshl.edu/pipermail/gmod-help/attachments/20101004/82e4ab27/attachment.html>