[Gmod-help] Re: [Gmod-gbrowse] ggb 1.71b using DAS server for the fasta sequences

[Scott Cain]

To add to this, and answer one of your other questions: you do not
absolutely need to have the dna sequences themselves to make gbrowse
work: all you really need is a gff file that describes the features.
You only need the dna sequence if you want to use the dna/gc content
glyph or provide translations either for the translation glyph or in
the cds glyph.

Scott


On Mon, Nov 9, 2009 at 5:54 PM, Dave Clements, GMOD Help Desk
<help at gmod.org> wrote:
> Hi Marc,
>
> I'm not an experienced DAS person, but I might be able to shed some
> light on the error message.  I believe the "chr?start:end reference is
> unknown!" error message is the result of not defining the whole
> chromosome somewhere.  From the tutorial
> (http://gmod.svn.sourceforge.net/viewvc/gmod/Generic-Genome-Browser/branches/stable/docs/tutorial/tutorial.html?content-type=text%2Fhtml#data_file):
>
> ---
> It is very important to have a full-length entry (such as the one for
> ctgA) for each reference sequence mentioned in the first column of the
> GFF3 file. However, the reference sequence can have any source and
> type you choose. Commonly used types are "clone", "chromosome" and
> "contig."
> ---
>
> I *think* you need to define the overall chromosome in a local database.
>
> Does anyone else have suggestions?
>
> Thanks,
>
> Dave C.
>
>
> On Thu, Nov 5, 2009 at 8:57 AM, Marc Wessner <mwessner at genoscope.cns.fr> wrote:
>> Hi,
>>
>> I have to install many private genome browsers that display specific
>> annotations on the human genome.
>>
>> I intend to configure a DAS server that could provide all the human
>> common tracks for all my genome browsers, so I don't have to copy the
>> whole genome fasta files and mRNA tracks data etc... several times.
>> First of all, am I right or the fasta files have to be present in each
>> browser database  ?
>>
>> In a browser that shall use the DAS server (but doesn't yet), I have
>> only loaded a few gff files : chromosome.gff, cytobands.gff and the
>> annotations.
>> Without the fasta files, when I try this genome browser alone, I get an
>> error message that says:"chr?start:end reference is unknown!" (what ever
>> the figures may be)
>>
>> Am I missing something ?
>> I am using this documentation:
>> http://gmod.svn.sourceforge.net/viewvc/gmod/Generic-Genome-Browser/branches/stable/docs/tutorial/tutorial.html?content-type=text%2Fhtml#DAS
>> Shall I look anywhere else ?
>>
>> Where could I find an explanation of how the region is defined:
>>  - Is chromosome.gff not enough to display the annotations for a given
>> region (I am not talking about bases or GC%) ?
>>  - Are fasta file madatory for such a purpose ?
>>  - Can the fasta sequences be part of what is gotten from the DAS in
>> order (I hope so)?
>>
>> Thanks for your hints,
>>
>> Best regards
>>
>> Marc
>>
>>
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>
>
>
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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