Re: [Gmod-help] about chado

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Re: [Gmod-help] about chado

Scott Cain
Hi Marcelo,

I'm cc'ing this to the schema mailing list; the help and devel mailing
lists can be removed from follow up messages.

If I understand you correctly, you already have a GFF3 file of rice
SNPs that you obtained by converting a GenBank file to GFF3, and you'd
like to load that into Chado and browse with GBrowse, is that right?
While you can do that, the question I have is, do you already have a
Chado database with rice data in it?  I don't know anything about the
rice data set, but I imagine it would be quite big, and I'm not sure
what you'd gain from putting it in Chado.  If you only want to browse
it in GBrowse, it would probably make more sense to put the data in a
Bio::DB::SeqFeature::Store database (using the bp_seqfeature_load.pl
script that comes with BioPerl).

Scott


On Fri, Oct 29, 2010 at 11:29 AM, Marcelo Goncalves Narciso
(Pesquisador) <[hidden email]> wrote:

> Hi people,
> good morning.
>
> I need to send data from rice SNPs (.gff3 file) and
> I try the command
>
>  sudo /usr/local/bin/gmod_bulk_load_gff3.pl --dbname chadodb --dbuser uuu
> --dbpass xxxx --dbhost localhost --organism  --gff riceVariety.gff3
>
> I would like to know if I have download archives .gbk from
> NCBI about OryzaSativa and transform it in .gff3 and load in the
> bank.
>
> How to send data from SNP and rice to chado and how I
> use Gbrowser with chado is my question.
>
> Thank you.
>
> Marcelo.
> --
> Embrapa Arroz e Feijao (http://www.cnpaf.embrapa.br)
>
>



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

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Re: [Gmod-help] about chado

Scott Cain
Hi Marcelo,

Please keep the schema mailing list copied on your email so other
people can help and the responses can be archived.

There is a tool that comes with BioPerl called bp_genbank2gff3.pl,
which generally works pretty well (though not always perfectly, be
sure to spot check the output).  I would guess on SNP data it should
work pretty well.  NCBI does provide GFF3 for some of their data but
in my experience, it is so horribly flawed that it is worse than
nothing.

For hooking your Chado instance up to GBrowse, you need the perl
module Bio::DB::Das::Chado, which you can get directly from cpan.  It
has some documentation that could help, as well as a sample config
file in the contrib/conf_files directory of the GBrowse2 distribution
called 07.chado.conf.

Scott


On Fri, Oct 29, 2010 at 12:41 PM, Marcelo Goncalves Narciso
(Pesquisador) <[hidden email]> wrote:

> Hi Scott,
>
> I have snps from other varieties, and it is
> possible to create .gff3 of these snps.
>
> My problem is how to create GFF3 files from
> Nipponbare .gbk and .gff files from NCBI.
> If GenBank has .GFF3 my problem is solved
> and I need only the address.
>
> After it, I need to insert these data in chado
> and show it using gbrowser (how to configure
> gbrowser to get data from chado?).
>
> These are my questions.
>
> Thank you so much for your answer.
>
> Marcelo.
>
> On Fri, 29 Oct 2010 12:11:29 -0400, Scott Cain wrote
>> Hi Marcelo,
>>
>> I'm cc'ing this to the schema mailing list; the help and devel
>> mailing lists can be removed from follow up messages.
>>
>> If I understand you correctly, you already have a GFF3 file of rice
>> SNPs that you obtained by converting a GenBank file to GFF3, and
>> you'd like to load that into Chado and browse with GBrowse, is that right?
>> While you can do that, the question I have is, do you already have a
>> Chado database with rice data in it?  I don't know anything about the
>> rice data set, but I imagine it would be quite big, and I'm not sure
>> what you'd gain from putting it in Chado.  If you only want to browse
>> it in GBrowse, it would probably make more sense to put the data in a
>> Bio::DB::SeqFeature::Store database (using the bp_seqfeature_load.pl
>> script that comes with BioPerl).
>>
>> Scott
>>
>> On Fri, Oct 29, 2010 at 11:29 AM, Marcelo Goncalves Narciso
>> (Pesquisador) <[hidden email]> wrote:
>> > Hi people,
>> > good morning.
>> >
>> > I need to send data from rice SNPs (.gff3 file) and
>> > I try the command
>> >
>> >  sudo /usr/local/bin/gmod_bulk_load_gff3.pl --dbname chadodb --dbuser uuu
>> > --dbpass xxxx --dbhost localhost --organism  --gff riceVariety.gff3
>> >
>> > I would like to know if I have download archives .gbk from
>> > NCBI about OryzaSativa and transform it in .gff3 and load in the
>> > bank.
>> >
>> > How to send data from SNP and rice to chado and how I
>> > use Gbrowser with chado is my question.
>> >
>> > Thank you.
>> >
>> > Marcelo.
>> > --
>> > Embrapa Arroz e Feijao (http://www.cnpaf.embrapa.br)
>> >
>> >
>>
>> --
>> ------------------------------------------------------------------------
>> Scott Cain, Ph. D.                                   scott at
>> scottcain dot net GMOD Coordinator (http://gmod.org/)
>>      216-392-3087 Ontario Institute for Cancer Research
>
>
> --
> Embrapa Arroz e Feijao (http://www.cnpaf.embrapa.br)
>
>



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

------------------------------------------------------------------------------
Nokia and AT&T present the 2010 Calling All Innovators-North America contest
Create new apps & games for the Nokia N8 for consumers in  U.S. and Canada
$10 million total in prizes - $4M cash, 500 devices, nearly $6M in marketing
Develop with Nokia Qt SDK, Web Runtime, or Java and Publish to Ovi Store
http://p.sf.net/sfu/nokia-dev2dev
_______________________________________________
Gmod-schema mailing list
[hidden email]
https://lists.sourceforge.net/lists/listinfo/gmod-schema