[Gmod-help] Unrecognized features/regions

[Scott Cain]

Hi Alex,

I'm cc'ing this to the GBrowse mailing list, as there are lots of
people on that list who are very helpful with GBrowse issues.  I don't
see exactly what is wrong either; perhaps you could attach a sample of
your GFF and your full conf file.

Scott


On Thu, Aug 19, 2010 at 10:19 PM, Alex Nguyen <alex.nguyenba at utoronto.ca> wrote:
> Hi,
>
> I successfully set-up Gbrowse for the SGD-made GFF3 file, and am trying to
> set-up a similar Gbrowse for the Saccharomyces bayanus genome.
>
> I created what looks to me like a legit GFF3 file and loaded the GFF3 using
> bp_seqfeature_load.pl (just as I did for the SGD-made GFF3 file).
>
> Here is an exert of the file:
> contig436    YGOB    contig    1    4804    .    .    .
>  ID=contig436;Name=contig436
> contig436    YGOB    gene    530    3064    .    +    .
>  ID=Sbay_436.2;Name=Sbay_436.2;Note=Ortholog%20assigned%20by%20YGOB:YML029W
> contig436    YGOB    gene    3478    3906    .    +    .
>  ID=Sbay_436.3;Name=Sbay_436.3;Note=Ortholog%20assigned%20by%20YGOB:YML030W
>
> The SQL database for both setup look virtually identical to me, but here are
> some relevant parts:
> typelist
> 1   contig:YGOB
> 2   gene:YGOB
>
> locationlist
> 18   contig436
>
> name
> 39    contig436   1
> 40    Sbay_436.2   1
> 41    Sbay_436.3   1
>
> feature
> 39    1    18    1    4804    0    1    0    1
> 40   2   18   530   3064   1   1   0   1
> 41   2   18   3478   3906   1   0   3   1
>
> I have a hard time tracing why simply searching for something like contig436
> fails (error type NOT_FOUND). My conf file is exactly the same as the
> working one except pointing to another database.
>
> Alex
>
>
>



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