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/



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___________________________________________________________
The Galaxy User list should be used for the discussion of
Galaxy analysis and other features on the public server
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