- galaxy-user - lists.galaxyproject.org

Extracting reads mapped from bwa mapping
by Austin Paul 06 Sep '11

06 Sep '11

Hello, I recently figured out how to filter the output bwa SAM file for flag type in order to determine the number of reads that were successfully mapped. My question is, I previously thought I could generate a pileup, then sum the number of counts for each base of the reference, and divide this number by the length of the reads (not exact if some reads are hanging over the edge of the reference sequence, but should be close?). But when I compare these methods, I get drastically different results. What am I missing? Thanks, Austin

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Gene Track
by Neal DeLuca 06 Sep '11

06 Sep '11

After using Mac, and clicking on view in Gen Track an error pops up saying: You're seeing this error because you have DEBUG = True in your Django settings file. Change that to False, and Django will display a standard 500 page. How are these setting changed? Neal

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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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wiggle file
by Richard Mark White 31 Aug '11

31 Aug '11

Hi, this should be simple but it is not..forgive the newbie question. i am doing chip-seq. bowtie>sam filter for mapped reads>MACS. i want to create a wiggle file that displays in ucsc, but when i choose the "WIG" option on macs, and then try to show it in UCSC, it treats each line of the created WIG file as a separate track, and obviously does not show it as a graph. is there a wiki page somewhere that can give me the basics? or can someone point me in the right direction? thanks. rich

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why the result files are empty ? and is java applet supported by galaxy system?
by liyanhui607 31 Aug '11

31 Aug '11

Hi All, We want to add a program “PhyML 3.0” to galaxy system. This software was for phylogenetic developed byhttp://www.atgc-montpellier.fr/phyml/binaries.php.It can run normally in Linux environment with a file for example named “sample” as input and two files automatically named “sample.phy_phyml_stats.txt” and “sample.phy_phyml_tree.txt” as outputs. However, after added it to galaxy system, we found that it can produce the right result files in directory "/var/we/galaxy-dist/database/files/000”, but they did not return to the web page where they are empty. So who can tell me what is wrong? Another question, is java applet supported by galaxy system? Thank you very much! Best Wishes! Yan-Hui Li

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August 30, 2011 Galaxy Development News Brief
by Jennifer Jackson 31 Aug '11

31 Aug '11

August 30, 2011 Galaxy Development News Brief http://galaxyproject.org/wiki/News%20Briefs/2011_08_30 Source: http://getgalaxy.org new: % hg clone http://www.bx.psu.edu/hg/galaxy galaxy-dist upgrade: % hg pull -u -r 949e4f5fa03a What's New ISMB/ECCB, BOSC, and 3DSIG 2011 Slides Recent Publications GalaxyProject.org Wiki Tool Shed Upcoming Events Updated & Improved Data Tools Visualization (Trackster) Workflows API Source Quotas Bug Fixes

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