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

where to get indexes for mapping tools
by Yury Bukhman 05 Apr '11

05 Apr '11

Hi, we have set up a Galaxy server for internal use. We would like to provide indexes for NGS mapping tools for a set of organisms that are relevant to our research. While bowtie has a repository of such indexes, other tools, e.g. bwa, don't seem to have one, so we have to build our own. Is there a repository of pre-built indexes for all mapping tools supported by Galaxy somewhere? Thanks. Yury -- Yury V. Bukhman, Ph.D. Associate Scientist, Bioinformatics Great Lakes Bioenergy Research Center University of Wisconsin - Madison 445 Henry Mall, Rm. 513 Madison, WI 53706, USA Phone: 608-890-2680 Fax: 608-890-2427 Email: ybukhman(a)glbrc.wisc.edu

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Around Pittsburgh on April 6? Attend the Intro to Galaxy Sessions @ Pitt
by Dave Clements 02 Apr '11

02 Apr '11

Hello all, Dan Blankenberg will be giving two workshops on Galaxy at the University of Pittsburgh on April 6. The presentations are open to the public. See below for details and please contact Dan, or Carrie Iwema at Pitt, if you have any questions. Thanks, Dave C. Intro to Galaxy http://galaxy.psu.edu/ Dan Blankenberg, PhD Center for Comparative Genomics & Bioinformatics Penn State University Galaxy allows you to do analyses you cannot do anywhere else without the need to install or download anything. You can analyze multiple alignments, compare genomic annotations, profile metagenomic samples & more... Wednesday 6th April *10 am – 12 pm Intro to Galaxy (general interest) * * * *2 pm - 4 pm Working w/NGS Data (advanced users) * University of Pittsburgh Falk Library Conference Room B You are welcome to bring your laptop. ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ Carrie L. Iwema, PhD, MLS Information Specialist in Molecular Biology Health Sciences Library System University of Pittsburgh 200 Scaife Hall 3550 Terrace St Pittsburgh, PA 15261 412-383-6887412-648-8819 (fax)iwema(a)pitt.eduwww.hsls.pitt.edu/molbio ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -- http://galaxy.psu.edu/gcc2011/ http://getgalaxy.org http://usegalaxy.org/

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Unsubscription
by Massimo 02 Apr '11

02 Apr '11

Hi, Is there a way to unsubscribe from Galaxy e-mail list? Please, let me know. Thanks Massimo Bionaz PhD Post-doctoral researcher Institute for Genomic Biology, University of Illinois 366 Animal Sciences Laboratory 1207 W. Gregory Dr. Urbana, IL 61801 USA Office Tel: 1-217-333-6189 Fax: 1-217-333-8286

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Galaxy server-FTP
by Sher, Falak 01 Apr '11

01 Apr '11

HI I would like to use Galaxy server to upload files via FTP. I seek help for, log in to the FTP server at main.g2.bx.psu.edu. I dont see ftp log in option there. help please ? Falak

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Brad Chapman 's tool
by Sher, Falak 01 Apr '11

01 Apr '11

Hi if any body is using "Calculates coverage from a BAM alignment file" tool at local Galaxy? regards, Falak

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Gene Fusion Detection Workflow
by Ryan Golhar 01 Apr '11

01 Apr '11

Hi - Has anyone developed a gene fusion detection workflow in Galaxy that they would care to share?

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Re: [galaxy-user] cufflinks FPKM
by Jeremy Goecks 01 Apr '11

01 Apr '11

If Cufflinks works without a reference GTF, then the problem is the mismatch b/t your GTF and your bam file. A couple things to check: (1) that your genome chrom names in F3.csfata match those in your GTF; if not, you'll need to modify your GTF to match the names in your fasta. (2) that your GTF is sorted as your BAM is sorted. If these issues don't solve your problem, it's best to use the Cufflinks help email that I noted in my previous email. Good luck, J. On Mar 31, 2011, at 10:32 AM, lishiyong wrote: > > Hello,I don't use Galaxy.But I have uploaded the file(sorted file 20:test_44.bam refgene.gtf : ) It's works OK without the reference GTF file ,while with reference, I can't gain the right results, I do these in my computer. > 2011-03-31 > lishiyong > 发件人： Jeremy Goecks > 发送时间： 2011-03-31 21:36:52 > 收件人： lishiyong > 抄送： galaxy-user > 主题： Re: [galaxy-user] cufflinks FPKM > Hello, > > It's not clear whether you're using Galaxy. If you're using Galaxy, please share you history with me (History Options --> Share/Publish --> Share with User --> my email) and I'll take a look; otherwise, Cufflinks has an email list for questions: tophat.cufflinks(a)gmail.com > > Best, > J. > > On Mar 31, 2011, at 3:39 AM, lishiyong wrote: > >> Hi: >> >> >> I gain the SOLiD sequencing data.I used bowtie to map human genome then I sort the sam file .I used cuffinks to calculate FPKM with the sam file ,human gtf file .it gives 0 FPKM values and this is for all genes .what's the reason? >> >> (1) bowtie -C human_hg18_color -f F3.csfasta -Q F3_QV.qual -v 2 -k 100 -p 6 --mapq --sam test.sam >> (2) samtools view -uS test.sam 2>/dev/null | samtools sort -m 2000000000 - test.bam >> (3) cufflinks -G refGene_hg18.gtf test.bam.bam >> 2011-03-31 >> lishiyong >> ___________________________________________________________ >> The Galaxy User list should be used for the discussion of >> Galaxy analysis and other features on the public server >> at usegalaxy.org. Please keep all replies on the list by >> using "reply all" in your mail client. For discussion of >> local Galaxy instances and the Galaxy source code, please >> use the Galaxy Development list: >> >> http://lists.bx.psu.edu/listinfo/galaxy-dev >> >> To manage your subscriptions to this and other Galaxy lists, >> please use the interface at: >> >> http://lists.bx.psu.edu/ > >

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cufflinks FPKM
by lishiyong 01 Apr '11

01 Apr '11

Hi: I gain the SOLiD sequencing data.I used bowtie to map human genome then I sort the sam file .I used cuffinks to calculate FPKM with the sam file ,human gtf file .it gives 0 FPKM values and this is for all genes .what's the reason? (1) bowtie -C human_hg18_color -f F3.csfasta -Q F3_QV.qual -v 2 -k 100 -p 6 --mapq --sam test.sam (2) samtools view -uS test.sam 2>/dev/null | samtools sort -m 2000000000 - test.bam (3) cufflinks -G refGene_hg18.gtf test.bam.bam 2011-03-31 lishiyong

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NR data for instantiation
by drhoads＠uark.edu 31 Mar '11

31 Mar '11

My IT people are setting us up for an instantiation of Galaxy on campus for my course and faculty to use. They have most everything working on our server but when I get to the Megablast there are no databases. I need to give them the instructions for how to set up for databases like NR and maybe the human HGTS. Where can I find that information to give to the people that will understand it? Douglas Rhoads, Professor of Biological Sciences Director of Graduate Program in Cell and Molecular Biology 601 SCEN, Dept. of Biological Sciences, 1 University of Arkansas, Fayetteville, AR 72701 drhoads(at)uark.edu, http://biscweb.uark.edu/drhoads phone: 479-575-3251 FAX: 479-575-4010

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aaChanges / BED-to-Codon
by Christopher Schroeder 31 Mar '11

31 Mar '11

Hello list, I already analysed some of our data with your framework and I want to thank you for your great work. But lately I stumbled on some strange behavior - I used the "aaChanges"-tool, as well as the Gene "BED-to-Codon"-tool with the same Gene-BED-File and compared the results. What I did: #example BED-file: chr17 3763624 3794037 uc002fwt.2 0 - 3765504 3788981 0 16 1953,104,129,88,74,54,200,89,22,37,134,52,54,48,403,51, 0,5577,9156,9470,12223,13078,15892,20015,21296,22197,22711,23098,23553,24049 ,24997,30362, #example-output of "aaChanges" chr17 3775847 3775848 C uc002fwt.2 Glu:Gly 375 T #example-output of "BED-to-Codon" chr17 3773172 3773175 uc002fwt.2 0 - chr17 3773175 3773178 uc002fwt.2 0 - chr17 3773178 3773181 uc002fwt.2 0 - chr17 3775849 3775852 uc002fwt.2 0 - chr17 3775852 3775855 uc002fwt.2 0 - Comparing both results, the "BED-to-Codon" actually presents no codon at position 3775848 - here the fist codon is starting at 3775849. But in fact, looking at the ucsc browser, "aaChanges" is right. There are another few examples (~5/1500 snps) and apparently most of them are positions among the first codon in an exon. Did anyone meet this problem before? What is my mistake? Thank you. Regards Chris

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