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
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,
On 9/1/11 4:42 AM, Anton Nekrutenko wrote:
I'm reposting this question to the galaxy-user mailing list.
> Dear Anton,
> I am a PhD student in the Matrin-Luther University Halle-Wittenberg focused on honey
> 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
). 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 Huang
> Institut für Biology/Zoologie, Molekulare Ökologie, Martin-Luther-Universität Halle
> 06099, Halle, Germany.
> Honeybee Research Institute, Jiangxi Agricultural University, 330045, Nanchang,
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