September 2011 - galaxy-user - lists.galaxyproject.org

Visualization > New Track Browser dropdown menu too long
by Kevin Lam 06 Sep '11

06 Sep '11

I found the dropdown menu list to be too long to be effectively used especially when viewed i chrome (browser) I can only see 5 genomes at a time and the ordering of the genomes isn't intuitive. Can I suggest that a frequently used genomes list be in the rest of the page so that it is easier to use for most users? like a table of common genomes to immediately create a new track browser from there? Cheers Kevin

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user specific access/options
by Petr Novak 01 Sep '11

01 Sep '11

Hi everybody, I am developing the application on Galaxy server. One of the requirement is to create user specific list of options. Is it possible to access somehow $__user_email__ in <options> tag or in <conditional> ?. I did not found documentation how to used cheetah in galaxy tool xml files but from files provided with galaxy, cheetah is used only in <command> and <config> tag. Is that rigth? If it can be used in any part of xml definition file it would make much easier to generate xml dynamicaly based on the $__user_email__ Does anybody have an idea how to manage this problem? Petr Novak

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Thanks from Di Nguyen. U of Washington
by Jennifer Jackson 01 Sep '11

01 Sep '11

Hello Di, Both Bowtie and Tophat will map sequences, with Tophat being preferred for RNA-seq data. If you wish to do downstream analysis, then using the Cuff* tools would be the next steps. Each of these tools has an associated help description that explains the inputs/outputs. Thanks for using Galaxy, Jen Galaxy team ps. Please send all questions directly to the mailing lists unless they contain private data/links. On 9/1/11 10:45 AM, Di Nguyen wrote: > Hi Jen, > > Thank you very much. I already used Galaxy to prepare the mapping by > bowtie for solid. I saw the tophat for solid on the test server and will > try it. Do I need to run cufflink after that? > > Please accept my utmost appreciation! > > Di -- Jennifer Jackson http://usegalaxy.org http://galaxyproject.org/Support

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Customize Annotated refgenome in Galaxy
by Anton Nekrutenko 01 Sep '11

01 Sep '11

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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RNAseq for Solid data
by Di Kim Nguyen 01 Sep '11

01 Sep '11

Hi, I needed help in crunching RNA-seqs done with solid platform. I have fasq files. Please give me the steps necessary in this process to get the fpkm from cufflink? This is mouse data. Thank you very much, please accept my appreciation. Di Nguyen U of Washington

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