- galaxy-user - lists.galaxyproject.org

Changing Bowtie parameters in TopHat
by Jeremy Coate 17 Nov '11

17 Nov '11

My apologies if this has been covered before but I am using Galaxy Main and wonder if, when running TopHat, you can modify the mapping parameters used by Bowtie? It seems that the full parameter list for TopHat pertains only to the reads that aren't mapped by Bowtie (the reads spanning splice junctions). Is there a way to access the full parameter list of Bowtie through TopHat? Or perhaps run Bowtie directly, then feed this into a TopHat run? Thanks, Jeremy

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RV: Visual and Conputational Analysis of positive sites in chip-chip data
by Mónica Pérez Alegre 17 Nov '11

17 Nov '11

Hi all We are working with chip-chip data of S. cerevisiae (from Affymetrix) and actually we have two problems and we don´t know if it´s possible to perform in Galaxy: 1. We use the tool intersect to get the annotation of positive genomic regions in our file bed. After, we need calculate statistical enrichments for associations between genomics regions and annotations. It´s this possible in Galaxy? 2. Other query. How plot for visual inspection enrichment ratio profile versus different sets of genomic loci (i.e.: tRNA, LTR,…) Best Regards, ☺If you have used the Services of the Genomics Unit of Cabimer, we would be grateful if you would give us a mention in future publications Mónica Pérez Alegre, PhD Genomics Unit CABIMER-CSIC Edif. CABIMER - Avda. Américo Vespucio s/n Parque Científico y Tecnológico Cartuja 93 41092 Seville-SPAIN Tlf: +34 954 467 828 Fax: +34 954 461 664 www.cabimer.es<http://www.cabimer.es/> http://www.cabimer.es/web/es/unidades-apoyo/genomica

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clipping from 5' end
by Soetkin Versteyhe 16 Nov '11

16 Nov '11

Hi all, Does anyone know if it is possible to trim/clip a sequence from the 5' end? Thank you. Best, Soetkin. Soetkin Versteyhe, PhD PostDoc University of Copenhagen Faculty of Health Sciences The Novo Nordisk Foundation Center for Basic Metabolic Research Integrative Physiology Blegdamsvej 3B 2200 København N Denmark PHONE +45 35337116 soetkin.versteyhe(a)sund.ku.dk http://sund.ku.dk http://metabol.ku.dk<http://metabol.ku.dk/> [cid:image001.gif@01CCA476.A4F86460]

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Regarding .exe file
by Shambhavi Srivastava 15 Nov '11

15 Nov '11

Dear Galaxy users, Is it possible to install .exe files in galaxy?If yes then how? Thanx, Shambhavi

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https://galaxy.jgi-psf.org/
by Chauhan, Archana 15 Nov '11

15 Nov '11

Dear Sir/Madam, I am registered with galaxy http://main.g2.bx.psu.edu/. But I recently came across another link as https://galaxy.jgi-psf.org/ . This has some very good applications especially w.r.t to the genome assembly (MIRA, velvet), microbial ecology (Mothur etc) and Stats/Graphing Tools. Overall this links seems much better than the Main galaxy and fulfils the general aspirations of a user. Is this link subscribed JGI and its collaborators OR any one can be a part of it. Is there any version of galaxy server wherein we can have these applications available for public use. Thank you. Regards, Archana Post-Doctoral Research Scholar, University of Tennesse Knoxville, USA

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trimming
by dtrejo＠ira.cinvestav.mx 14 Nov '11

14 Nov '11

Does anyone know if it is possible to trim sequencing adaptor sequences away in Galaxy? and what is the necessary format for trimming sequences? because in Clip adapter sequences I can not to see my files. thaks Diana Trejo, PhD -- This message has been scanned for viruses and dangerous content by MailScanner, and is believed to be clean.

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Trouble in extracting species on maf imported from UCSC
by 4urelie K 14 Nov '11

14 Nov '11

Hi, When I import a multiz46way maf alignement from UCSC, if is is a whole chromosome, then when I try to "Filter MAF blocks by Species" the list of species does not appear. If I import a small region, it works... Is it a question of size? Although it seems OK when I look at it, could it be a problem in the maf format that I could solve? Thank you, Aurelie

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Asynchronous data source
by Joachim Baran 14 Nov '11

14 Nov '11

Hello! I am adding support for Galaxy's asynchronous data sources to a server of mine, but I cannot get Galaxy to retrieve the actual data from it. So far, I have added a data source tool to my Galaxy installation which links out to my server. There I track the URL that is provided by Galaxy and later I use this URL to tell Galaxy that the data can be retrieved. At this point, Galaxy returns an HTML document to me, which says (excerpt): "[...] <p>The following job has been successfully added to the queue:</p> <div style="padding: 10px"><b> 1: testserver</b></div> <p> You can check the status of queued jobs and view the resulting data by refreshing the <b>History</b> pane. When the job has been run the status will change from 'running' to 'finished' if completed successfully or 'error' if problems were encountered. </p> [...]" I just discard this HTML. When I then go back to my Galaxy server, nothing has happened. Even when I refresh, I do not see any job pending. Does anyone know why Galaxy would not retrieve the data? Do I really have to show the HTML that is returned by Galaxy to make it work? Thanks, Joachim

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Re: [galaxy-user] Lastz
by Nate Coraor 14 Nov '11

14 Nov '11

On Nov 11, 2011, at 10:01 AM, Andrew South wrote: > Thanks Nate, hope it's a quick fix. Best wishes, Andy Hi Andy, All backlogged NGS jobs should now be running, new ones will likely queue until free slots are available. Please let us know if there's further trouble, and thanks for using Galaxy, --nate > > ************************************************************ > Please consider the environment. Do you really need to print this email? > > > >>> Nate Coraor <nate(a)bx.psu.edu> 11/11/2011 14:55 >>> > On Nov 11, 2011, at 9:21 AM, Andrew South wrote: > > > Hello folks > > > > Anyone else having trouble with running Lastz to map? > > > > Jobs are being sent but not running. > > > > It stopped working for me two days ago after working perfectly, I've tried fiddling with the formats but no joy. > > Hi Andy, > > It looks like there's a problem with the cluster that runs our NGS jobs. I'm currently looking into it. Sorry for the inconvenience. > > --nate > > > > > Thanks, > > > > Andy > > > > > > Dr A P South > > Centre for Oncology and Molecular Medicine > > University of Dundee > > Ninewells Hospital & Medical School > > Dundee > > DD1 9SY > > Tel 01382 496432 > > Fax 01382 633952 > > > > a.p.south(a)dundee.ac.uk > > > > > > ************************************************************ > > Please consider the environment. Do you really need to print this email? > > > > The University of Dundee is a registered Scottish charity, No: SC015096 > > > > ___________________________________________________________ > > 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/ > > > The University of Dundee is a registered Scottish charity, No: SC015096 >

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generic filenames with Export to File
by Danielle Lemay 14 Nov '11

14 Nov '11

Hello, When using Export to File, it appears that galaxy renames each output file to something generic datXXX.dat and changes the filename extension (to .dat). How do I convince Galaxy to preserve my filenames so I know which file is which ? Is there some other way to download multiple output files and preserve their names and file extensions? Thanks, Danielle ######################################################### Danielle G. Lemay, PhD Assistant Professional Research Scientist, UC Davis Genome Center University of California at Davis (530) 220 3438 dglemay(a)ucdavis.edu

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