Customize Annotated refgenome in Galaxy
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/
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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Anton Nekrutenko -
Jennifer Jackson