Customize Annotated refgenome in Galaxy

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Customize Annotated refgenome in Galaxy

Anton Nekrutenko
Qiang:

I'm reposting this question to the galaxy-user mailing list.

Thanks!

anton

> Dear Anton,
>
> I am a PhD student in the Matrin-Luther University Halle-Wittenberg focused on honey bee Ecology.
>
> Galaxy is a very flexible tool to do RNA Seq analysis. I have a problem and need your help. The galaxy provide build in annotated reference genome of honey bee (2005). This is a old version and the lastest version (2011) has much higher resolution (http://www.ncbi.nlm.nih.gov/nuccore?term=CM000054:CM000069[PACC]). I tried to bulid a customized annotated reference genome. First, I upload the annotated reference genome (.gb file), but can not choose it when I map the read (Tophat for Illumina). Then I upload the reference genome without annotation (.fasta file), it works. But I need the annotation of the genes to analyze the differencial expression.
>
> We are very interested in galaxy and use it in our research analysis. Hope you can help us solve this problem.  
>
> Expecting your reply!
>
> All the best,
> Qiang
>
> ****************************************
> Qiang Huang
> Institut für Biology/Zoologie, Molekulare Ökologie, Martin-Luther-Universität Halle -Wittenberg  
> 06099, Halle, Germany.
> Honeybee Research Institute, Jiangxi Agricultural University, 330045, Nanchang, China.
> http://www.mol-ecol.uni-halle.de/staff/huang-q/
>


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Re: Customize Annotated refgenome in Galaxy

Jen Hillman-Jackson
Hello Qiang,

The best solution is to use the fasta version of the reference genome
when running the Galaxy analysis tools and then link back in the
annotation as needed using the tool "Join, Subtract and Group -> Column
Join".

This would require you to covert/load the genbank .gb data in tabular
format and possibly to use some of the tools in "Text Manipulation".
Galaxy currently does not have a genbank .gb file converter, but a quick
web search brings up several options for you to choose from.

We hope this helps to get you started,

Best,

Jen
Galaxy team

On 9/1/11 4:42 AM, Anton Nekrutenko wrote:

> Qiang:
>
> I'm reposting this question to the galaxy-user mailing list.
>
> Thanks!
>
> anton
>
>> Dear Anton,
>>
>> I am a PhD student in the Matrin-Luther University Halle-Wittenberg focused on honey bee Ecology.
>>
>> Galaxy is a very flexible tool to do RNA Seq analysis. I have a problem and need your help. The galaxy provide build in annotated reference genome of honey bee (2005). This is a old version and the lastest version (2011) has much higher resolution (http://www.ncbi.nlm.nih.gov/nuccore?term=CM000054:CM000069[PACC]). I tried to bulid a customized annotated reference genome. First, I upload the annotated reference genome (.gb file), but can not choose it when I map the read (Tophat for Illumina). Then I upload the reference genome without annotation (.fasta file), it works. But I need the annotation of the genes to analyze the differencial expression.
>>
>> We are very interested in galaxy and use it in our research analysis. Hope you can help us solve this problem.
>>
>> Expecting your reply!
>>
>> All the best,
>> Qiang
>>
>> ****************************************
>> Qiang Huang
>> Institut für Biology/Zoologie, Molekulare Ökologie, Martin-Luther-Universität Halle -Wittenberg
>> 06099, Halle, Germany.
>> Honeybee Research Institute, Jiangxi Agricultural University, 330045, Nanchang, China.
>> http://www.mol-ecol.uni-halle.de/staff/huang-q/
>>
>
>
> ___________________________________________________________
> 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/
>

--
Jennifer Jackson
http://usegalaxy.org
http://galaxyproject.org/Support
___________________________________________________________
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/
Jennifer Hillman-Jackson
http://galaxyproject.org