[Gmod-help] sample conf file for contig alignments?

[Zhiliang Hu]

Thanks Scott for your quick reply.

I feel hesitate to ask on the list because this appear to be a straight-forward problem, and maybe it's only me a slow learner.

I have a set of cattle genome assembly files (chrNN.fa; chrNN.agp; contigs.all.fa; etc). I have created .gff files from each .agp files using a script from Justin of Elsik's group, loaded to MySQL db with the bulk loader tool, and made database connections, etc.

 > bp_bulk_load_gff.pl -u xx -p xx -d gb_cattle chr8.gff chr8.fa

However I simply don't see the chromosome track graph: http://www.animalgenome.org/cgi-bin/gbrowse/cattle/ - It seems to me an incomplete configuration problem (I tried existing conf files, e.g. the "Honey Bee" example is connected to this new "cattle" db).

I may be wrong but I tried to track info flow from gff/fasta files to config but not sure:
how each record in the gff file can be linked to sequences or there should not be (column 9's "group" info is sufficient?)

I have scrolled through Lincoln's tutorial and "Configuration HOWTO" but don't seem to follow (1) how each section is defined to function for, and (2) how each section is related? (seems "aggregators" contain what sub-sections to show? etc).

I am not sure where exactly I am lost ...

Zhiliang


At 03:45 PM 9/22/2008 -0400, Scott Cain wrote:
>Hi Zhiliang,
>
>I'm not really sure what you are looking for.  Is your data similar to
>what you might find in the tutorial?  Also, when looking for config
>file help, it is generally a good idea to write to the GBrowse mailing
>list, https://lists.sourceforge.net/lists/listinfo/gmod-gbrowse ,
>because it is a well subscribed list with lots of people who know
>config files inside and out.
>
>Scott
>
>
>On Mon, Sep 22, 2008 at 3:25 PM, Zhiliang Hu <zhu at iastate.edu> wrote:
>> Dear Dave or Scott,
>>
>> I have managed to load a cattle chromosome contigs (GFF) to GBrowse database (MySQL), but I don't seem to see expected contig alignments... wonder could you share an example configuration file for contig alignments? (I searched for but failed to find one :)
>>
>> Thank you,
>>
>> Zhiliang