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

window and merge workflow?
by zod 20 Oct '10

20 Oct '10

Hi, I have two datasets, both from the same cell type and same genome build. One data set is chip-seq, windowed at either 1MB or 100Kb. The other is from a tiled array, with probes placed ~2-3kb apart. I want to window the latter at either 100Kb or 1Mb (an averaging of the values will suffice), and then intersect the two data sets so that for each window I'll have two data points: the chip-seq and the tiled array values. It seems like this should be possible using Galaxy, but I'm struggling with what the workflow should be. Does anyone have a workflow, or suggestions? Thanks in advance, David

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Troubles with Batch download
by Cristian Rojas 20 Oct '10

20 Oct '10

Hi everybody, sorry for bother youwith a silly question. I have a list with a LOT of rice loci (LOC_Os...) uploaded to Galaxy as a unique file, and would like to obtain just the sequence of them. I tried to use the Gramene, but I couldnt. Any tip? Thanks Cristian

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running galaxy jobs on pbs pro cluster
by Laure QUINTRIC 19 Oct '10

19 Oct '10

Hello, I'm having some troubles installing pbs_drmaa-1.0.2.tar.gz (http://sourceforge.net/projects/pbspro-drmaa/) with pbs pro (./configure fails). Have anyone already succeeded in installing galaxy to run jobs on pbs pro ? Thanks, Laure -- Laure QUINTRIC Ifremer - IDM/RIC Technopôle Brest-Iroise 29280 Plouzané Tel: 02 98 22 49 11 - Fax : 02 98 22 46 47 E-mail : Laure.Quintric(a)ifremer.fr

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Re: [galaxy-user] concerning: "All SNPs in Personal Genomes"
by Greg Von Kuster 14 Oct '10

14 Oct '10

Hello Oskar, "N" in the file "All SNPs in Personal Genomes" implies lack of information. The file has SNP data from the Southern African genomes as well as a lot of other published personal genomes. For the other personal genomes, we did not have the consensus calls at all locations (we just have the SNP locations and calls) and hence that lack of information is depicted by the base "N". For the Southern African genomes, the lack of information could be because of the method used e.g. genotyping does not give the consensus call on every location, or because we had no coverage on that location. In the future, please send Galaxy questions / correspondence to one of the Galaxy mail lists ( galaxy-dev(a)bx.psu.edu, galaxy-user(a)bx.psu.edu, galaxy-bugs(a)bx.psu.edu ) instead of my personal email address. Thanks! On Oct 14, 2010, at 5:00 AM, Oskar Hallatschek wrote: > Dear Greg, > > could you please let me know whether an entry "N" in the file "All SNPs in Personal Genomes" refers to an unidentifiable base, > and why there are so many such entries in the displayed Genome. > > many thanks, > Oskar > -- > Oskar Hallatschek > MPI for Dynamics and Self-Organization > Biological Physics and Evolutionary Dynamics > Bunsenstr. 10, D 37073 Goettingen > phone: +49-551-5176-670 > fax: +49-551-5176-669 > e-mail: oskar.hallatschek(a)ds.mpg.de > http://www.evo.ds.mpg.de/ > Greg Von Kuster Galaxy Development Team greg(a)bx.psu.edu

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Re: [galaxy-user] running R in Galaxy
by Freddy 14 Oct '10

14 Oct '10

Following the discussion on this topic, the solution: You can run R 'straight' in galaxy without a wrapper: <command>R --slave --vanilla --file=$GALAXY_ROOT_DIR/tools/Rscript --args $infile $outfile</command> The input is never a big problem in galaxy, but how to capture the output was not so clear to me. So, Make sure your output file can be seen by galaxy (which was basically my problem): <inputs> <param name="infile" type="data" format="tabular"/> </inputs> <outputs> <data name="outfile" type="data" format="tabular"/> </outputs> And in R making sure, the output file has a name as well: write.table(data, sep="\t", file=out.file, row.names=F) Thanks for all the help!!

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LastZ on galaxy
by Inbar Plaschkes 13 Oct '10

13 Oct '10

Dear galaxy team, I would like to know whether it is possible to perform LastZ (multiple sequence alignment tool for aligning different genomes to each other) ? if so then how ? is there a tutorial you can refer me to ? many thanks Inbar -- ______________________________________________________________ Inbar Plaschkes Bioinformatics Core Facility National Institute for Biotechnology in the Negev Building 51, room 314 Ben-Gurion University of the Negev Beer-Sheva 84105, Israel Email: inbar.plaschkes(a)gmail.com Tel: 08-6479034 054-7915931 Fax: 08-6472983 http://bioinfo.bgu.ac.il

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sorter function failure
by Freddy 13 Oct '10

13 Oct '10

Dear Galaxy team, the sorter function under filters has a defect: it only ever sorts on the c1 column always in ascending order, alphabetical style We tried many times with a test data file. However, it DOES work on the main.g2.bx.psu.edu site. So, the local galaxy-dist is the problem. Could you please look at this and correct it? Kind regards, Freddy de Bree

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how to cancel a upload to data library?
by Kevin Lam 13 Oct '10

13 Oct '10

Hi, I have made a mistake of uploading via file browser a large file through the data library function. How do I cancel it as it resumes upload whenever I start the local instance. Cheers Kevin

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extracting sequence from 2bit files
by Amit Indap 12 Oct '10

12 Oct '10

Hi Galaxy team: Apologies if this is the wrong place to post this question, but is there an API in bx-python that I can use to extract sequence out of a 2bit file? Thanks for your help, Amit -- Amit Indap

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Affymetrix pig array re-annotation
by Lavinia Gordon 11 Oct '10

11 Oct '10

Hi Lara, Have you seen this: http://www4.ncsu.edu/~stsai2/annotation/ They have updated their annotation in 2010. with regards, Lavinia. > ------------------------------ > > Message: 2 > Date: Wed, 6 Oct 2010 09:13:09 +0200 > From: "NONELL MAZELON, LARA"<lnonell(a)imim.es> > To: "galaxy-user(a)bx.psu.edu"<galaxy-user(a)bx.psu.edu> > Subject: [galaxy-user] Reannotate microarray data > Message-ID: > <BB3B87345736EE45843CC0ADF9EEEB0D2AE8CD85CE(a)hermes2.imim.es> > Content-Type: text/plain; charset="us-ascii" > > Dear Galaxy team, > > I just discovered your tool and is fantastic!. I want to reannotate the porcine affymetrix microarray. So I wanted to perform the following steps: > > 1. Run blat/blast to the porcine genome SGSC sscrofa9.2/susScr2 with the sequences of all probes on the array (which i have in a csv file) > 2. Get genes > 3. Do the same with human genome > > I can load my file and the entire pig genome but i do not know how to perform the "alignment" > Is it possible to perform blat/blast (or any other alignment tool similar) through Galaxy? > > Thanks very much in advance, > > <mailto:lnonell@imim.es>Lara Nonell > Microarray Analysis Service > Scientific and Technical Services > IMIM-Hospital del Mar > > Barcelona Biomedical Research Park (office 166) > Doctor Aiguader, 88 | 08003 Barcelona > Tel.+34 933 160 577 | Fax +34 933 160 410 > lnonell(a)imim.es<mailto:lnonell@imim.es> > www.imim.es<http://www.imim.es/> > >

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