July 2010 - galaxy-user - lists.galaxyproject.org

Rhesus Macaque genome in lastz
by Lakshmanan Iyer 20 Jul '10

20 Jul '10

Hi In the NGS mapping option with "lastz" I cannot find the Rhesus Macaque genome. The web site says: "If your genome of interest is not listed, contact the Galaxy team" Could you please make this reference genome available? Rhesus Jan. 2006 (MGSC Merged 1.0/rheMac2) assembly -best -Lax

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Swine genomes for NGS tools
by Kelly Vincent 20 Jul '10

20 Jul '10

Jeff, Two swine genomes have been added to the NGS tools. These are the build 9.58 you specifically requested (listed as Scrofa9.58) and also the susScr2 (Nov. 2009, available from UCSC). Let us know if you run into any problems using either. Regards, Kelly

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problems accessing the data
by research pal 20 Jul '10

20 Jul '10

Dear galaxy, I am not able to get the requisite output when I try the option with the output format "selected fields from primary and related tables" which then asks me to customize from the hg18.KgXref fields. The error message that I am getting is "Can't find route from wgEncodeBroadChipSeqPeaksHmecCtcf to kgXref via all.joiner ". Could you please help ? warm regards, Amit.

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Galaxy Developer Conference 2011
by Anton Nekrutenko 19 Jul '10

19 Jul '10

Dear members of Galaxy Community: We are starting to prepare for the Second Galaxy Developer Conference in 2011. This time we would like to hold it in Europe and we were asked to consider Uppsala and Heidelberg. However, Galaxy is a community project and we would like to ask you for input. If any of you knows good and reliable conference facility, please let us know. We will then research this and finalize the conference planning. So let us know... Thanks, anton + galaxy team Anton Nekrutenko http://nekrut.bx.psu.edu http://usegalaxy.org

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Re: [galaxy-user] [galaxy-bugs] Galaxy tool error report from azovoil@gwdg.de
by Jeremy Goecks 18 Jul '10

18 Jul '10

>> >> Error: this SAM file doesn't appear to be correctly sorted! >> >> >> Could you please add also the function from cufflinks for sorting sam file before use? > > Given that you're not using Tophat to map your reads, you'll want to sort your reads before uploading them to Galaxy b/c Galaxy does not (yet?) have a tool to sort SAM files. [cc'ing galaxy-user as this may be useful information to other users.] Hi Zovoilis, I was mistaken in writing that Galaxy cannot sort SAM files. Galaxy can sort SAM files; here is an example history that illustrates the sorting of a SAM file: http://test.g2.bx.psu.edu/u/jeremy.goecks/h/sorting-sam-file-for-cufflinks There are two steps in sorting a SAM file: (1) removing SAM headers via the 'remove lines from beginning of a file' tool and (2) using the 'sort data in ascending or descending order' tool to sort by chromosome name and then by position. Samtools provides a single-step process for sorting SAM files, and we expect to add this capability to Galaxy in the future so that the above 2-step process can be replaced by this single step. Best, J.

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July 16, 2010 Galaxy Development News Brief
by Greg Von Kuster 16 Jul '10

16 Jul '10

The latest news brief is available at the following link. http://bitbucket.org/galaxy/galaxy-central/wiki/Features/DevNewsBrief/2010_… Greg Von Kuster Galaxy Development Team greg(a)bx.psu.edu

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microRNA Seq data workflow analysis
by Ana Sevilla 15 Jul '10

15 Jul '10

Dear Galaxy users. I would like to use Galaxy software for my microRNA data analysis. Could someone share with me the workflow I should use? Thank you very much in advance. Ana * * -- Ana Sevilla Hernandez Mount Sinai School of Medicine. 1425 Madison Ave. (Icahn Building) Floor 13. Room 26 Phone: (001) 212 659 8251 E-mail: Ana.Sevilla(a)mssm.edu

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Fwd: Install local copy of GALAXY
by Anton Nekrutenko 14 Jul '10

14 Jul '10

Begin forwarded message: > From: "Phang, Tzu" <Tzu.Phang(a)ucdenver.edu> > Date: July 14, 2010 4:09:40 PM EDT > To: "anton(a)bx.psu.edu" <anton(a)bx.psu.edu> > Subject: Install local copy of GALAXY > > HI ANTON, > > Great GALAXY discussion session at ISMB2010 in Boston. Our sequencing core lab is very interested in installing a local copy of GALAXY for our analysis needs. Could you lead me to the right direction about where I should start? > > Thanks > > Tzu Lip Phang PH.D > Assistant Professor > > Division of Pulmonary Sciences and Critical Care Medicine > University of Colorado Denver > Anschutz Medical Campus > Research 2, Box C272, 9th Floor > 12700 East 19th Avenue > Aurora, CO 80045 > > Office: 303-724-6057 > Fax : 303-724-6042 > Cell : 720-635-6323 Anton Nekrutenko http://nekrut.bx.psu.edu http://usegalaxy.org

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Re: [galaxy-user] Install local copy of GALAXY
by Anton Nekrutenko 14 Jul '10

14 Jul '10

Tzu: Look at http://getgalaxy.org Thanks, anton On Jul 14, 2010, at 4:09 PM, Phang, Tzu wrote: > HI ANTON, > > Great GALAXY discussion session at ISMB2010 in Boston. Our sequencing core lab is very interested in installing a local copy of GALAXY for our analysis needs. Could you lead me to the right direction about where I should start? > > Thanks > > Tzu Lip Phang PH.D > Assistant Professor > > Division of Pulmonary Sciences and Critical Care Medicine > University of Colorado Denver > Anschutz Medical Campus > Research 2, Box C272, 9th Floor > 12700 East 19th Avenue > Aurora, CO 80045 > > Office: 303-724-6057 > Fax : 303-724-6042 > Cell : 720-635-6323 Anton Nekrutenko http://nekrut.bx.psu.edu http://usegalaxy.org

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is there an equivalent of IGV or samtools tview?
by Michael Yourshaw 14 Jul '10

14 Jul '10

Is there a way on the public Galaxy to look at read alignments in bam files (or any other format) equivalent to IGV or samtools tview? (preferably not actually using buggy tview) ॐ Michael Yourshaw UCLA Geffen School of Medicine Department of Human Genetics, Nelson Lab 695 Charles E Young Drive S Gonda 5554 Los Angeles CA 90095-8348 USA myourshaw(a)ucla.edu 970.691.8299 This message is intended only for the use of the addressee and may contain information that is PRIVILEGED and CONFIDENTIAL, and/or may contain ATTORNEY WORK PRODUCT. If you are not the intended recipient, you are hereby notified that any dissemination of this communication is strictly prohibited. If you have received this communication in error, please erase all copies of the message and its attachments and notify us immediately. Thank you.

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