Re: [galaxy-user] New Genome Load Request

[Mark Guiltinan]

Guru

Yes please include, in fact they may be all that is needed?  They represent the 
assembled contigs and scaffolds that were linked to the genetic map and this 
represent the chromosomes...   I believe that they contain most of the contigs 
and scaffolds so there is redundancy.  there is one Tc0 that represents the 
unassembled contigs and scaffolds left over after assembling the 10 
pseudochromosomes that represent each of the 10 cacao chromosomes.  Yopu could 
see how this is on the gbrowse at the below website.

Regards

Mark


On Jan 26, 2012, at 10:39 AM, Guru Ananda wrote:

> Dear Mark,
> 
> Sorry for the delay in response.
> We're wondering whether or not to include pseudomolecules (along with contigs 
> and scaffolds) as genomic sequence for cacao genome. Can you kindly clarify 
> this?
> 
> Thanks,
> Guru.
> 
> 
> On Thu, Oct 27, 2011 at 4:08 PM, Mark Guiltinan  wrote:
> Hello Galaxy,
> 
> Would you please perform the following new genome load?
> 
> Theobroma cacao
> 
> All the necessary resource files can be found and downloaded at:
> 
> 
> http://cocoagendb.cirad.fr/gbrowse/download.html
> 
> Thank you
> 
> Mark Guiltinan
> 
> 
> 
> 
> Mark Guiltinan
> Professor of Plant Molecular Biology
> Penn State University 
> Department of Horticulture
> 422 Life Sciences Building
> University Park, PA 16802-5807
> Phone  814 863-7957   
> m...@psu.edu
> Web Site: http://guiltinanlab.cas.psu.edu
> 
> 
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> 
> 
> -- 
> Graduate student, Bioinformatics and Genomics
> Makova lab/Galaxy team
> Penn State University
> 505 Wartik lab
> University Park PA 16802
> g...@psu.edu
> 

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Re: [galaxy-user] New Genome Load Request

[Guru Ananda]

Dear Mark,

Sorry for the delay in response.
We're wondering whether or not to include pseudomolecules (along with
contigs and scaffolds) as genomic sequence for cacao genome. Can you kindly
clarify this?

Thanks,
Guru.


On Thu, Oct 27, 2011 at 4:08 PM, Mark Guiltinan  wrote:

> Hello Galaxy,
>
> Would you please perform the following new genome load?
>
> Theobroma cacao
>
> All the necessary resource files can be found and downloaded at:
>
>
> http://cocoagendb.cirad.fr/gbrowse/download.html
>
> Thank you
>
> Mark Guiltinan
>
>
>
>
>  Mark Guiltinan
> Professor of Plant Molecular Biology
> Penn State University
> Department of Horticulture
> 422 Life Sciences Building
> University Park, PA 16802-5807
> Phone  814 863-7957
> m...@psu.edu
> Web Site: http://guiltinanlab.cas.psu.edu
>
>
> ___
> The Galaxy User list should be used for the discussion of
> Galaxy analysis and other features on the public server
> at usegalaxy.org.  Please keep all replies on the list by
> using "reply all" in your mail client.  For discussion of
> local Galaxy instances and the Galaxy source code, please
> use the Galaxy Development list:
>
>  http://lists.bx.psu.edu/listinfo/galaxy-dev
>
> To manage your subscriptions to this and other Galaxy lists,
> please use the interface at:
>
>  http://lists.bx.psu.edu/
>



-- 
Graduate student, Bioinformatics and Genomics
Makova lab/Galaxy team
Penn State University
505 Wartik lab
University Park PA 16802
g...@psu.edu
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Re: [galaxy-user] New Genome Load Request

[Jennifer Jackson]

Hi Mark,

We'll try to get this in ASAP - thank you for sending the source 
information. When on the Main server, I will send you an update email.


Take care,

Jen
Galaxy team

On 10/27/11 1:08 PM, Mark Guiltinan wrote:

Hello Galaxy,

Would you please perform the following new genome load?

Theobroma cacao

All the necessary resource files can be found and downloaded at:


http://cocoagendb.cirad.fr/gbrowse/download.html

Thank you

Mark Guiltinan




Mark Guiltinan
Professor of Plant Molecular Biology
Penn State University
Department of Horticulture
422 Life Sciences Building
University Park, PA 16802-5807
Phone 814 863-7957
m...@psu.edu 
Web Site: http://guiltinanlab.cas.psu.edu



___
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at usegalaxy.org.  Please keep all replies on the list by
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--
Jennifer Jackson
http://usegalaxy.org
http://galaxyproject.org/wiki/Support
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