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

Gene Ontology Help
by Nicole Lynn Jacobs 18 Nov '11

18 Nov '11

To Whom it May Concern: My name is Nicole McDaniels. I am a Ph.D. candidate at Syracuse University. I am attempting to use RNAseq to look at changes in the transcriptome of zebrafish embryos upon morpholino injection. I have been using Galaxy Main to manage my data thus far. Recently, I completed the cufflinks/cuffcompare/cuffdiff analysis. I now have cuffdiff files in the tabular format. I would like to assess the gene ontologies of the differentially expressed transcripts, but I'm having trouble figuring out how to transfer over to GO Galaxy and then what exactly I should be doing in GO Galaxy. Is there a different program or server that would be better/easier for the gene ontology analysis than GO Galaxy? I've also looked at the GOseq R package, but again I'm not sure about the tabular file format or how to change it to a more appropriate format. Any help you can give me with this would be greatly appreciated. I thank you in advance for your time. All the best, Nicole McDaniels Ph.D Candidate Syracuse University Department of Biology

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combine data
by dongdong zhaoweiming 18 Nov '11

18 Nov '11

Hi, Can galaxy combine lots of data into a single file using "cat"? I have a 2GB sam type data, but I can't upload it by URL under my condition, so I want to spilt it into three files and upload it to galaxy and then combine it? Thanks a lot!weimin zhao

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GATK
by Metge, Franziska 17 Nov '11

17 Nov '11

Dear happy users of Galaxy, We are running Galaxy locally. It's a very fine tool! By now everything works fine, except when I try to run any GATK program. I usually get this error message: ##### ERROR ------------------------------------------------------------------------------------------ ##### ERROR A USER ERROR has occurred (version 1.3-14-g348f2db): ##### ERROR The invalid arguments or inputs must be corrected before the GATK can proceed ##### ERROR Please do not post this error to the GATK forum ##### ERROR ##### ERROR See the documentation (rerun with -h) for this tool to view allowable command-line arguments. ##### ERROR Visit our wiki for extensive documentation http://www.broadinstitute.org/gsa/wiki ##### ERROR Visit our forum to view answers to commonly asked questions http://getsatisfaction.com/gsa ##### ERROR ##### ERROR MESSAGE: The fasta file you specified (/tmp/tmpp0oxJu/hg19) does not exist. ##### ERROR ------------------------------------------------------------------------------------------ my picard_index.loc line for the hg19 reference looks like this: hg19 hg19 hg19 hg19 /drive1/galaxy/reference/hg19/sam_index/hg19_ref.fa gatk also the bam file I am submitting to GATK has the reference genome specified in it's attributes. Could please anyone help me. Thank you Franzi

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Tools appearing without inputs in workflow editor
by Paul-Michael Agapow 17 Nov '11

17 Nov '11

A peculiar bug, presented for your input: A colleague has built a few tools and is trying to incorporate them into a workflow. However: 1. When he creates an new empty workflow, edits it and adds the tools, they appear without inputs (i.e. the icons/boxes on the diagram have no input "sockets") 2. When he tries to save a history using these tools as a workflow, a error results in which Galaxy complains about an unrecognised name, being one of the tool inputs. Depending on which tool he includes in the workflow, the missing name occurs in whichever tool is earlier in the workflow. (Traceback available on request) Puzzling. And even more puzzling when I tried to debug this: 1. Other tools (not written by him) behave in the workflows as expected. 2. Pulling a copy of his config file across to my own instance of Galaxy and creating a dummy tool to house it, it worked perfectly 3. We're running the same version of Galaxy, albeit different versions of Python (2.5 vs 2.6.4) 4. The tools work fine in normal analysis mode. 5. Line-ending unix, XML seems to parse fine. I'm stymied here and unsure what to look at next. Ideas? ---- Paul Agapow (paul-michael.agapow(a)hpa.org.uk) Bioinformatics, Health Protection Agency ----------------------------------------- ************************************************************************** The information contained in the EMail and any attachments is confidential and intended solely and for the attention and use of the named addressee(s). It may not be disclosed to any other person without the express authority of the HPA, or the intended recipient, or both. If you are not the intended recipient, you must not disclose, copy, distribute or retain this message or any part of it. This footnote also confirms that this EMail has been swept for computer viruses, but please re-sweep any attachments before opening or saving. HTTP://www.HPA.org.uk **************************************************************************

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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 16 Nov '11

16 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 14 Nov '11

14 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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