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by gaurav thareja 13 Nov '11

13 Nov '11

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Cufflinks Annotation problem
by Bidwell, Christopher A. 12 Nov '11

12 Nov '11

Colleagues, I am having trouble running cufflinks with an annotation file on the public Galaxy. The assembled transcripts gtf file has all the FPKM at 0 although the gene expression and transcript expression tab files have values for FPKM. I have seen the SEQanswers threads about the compatibility of tophat bam files relative to chromosomes labeled as 1,2,3… versus Chr1, Chr2, Chr3… I am using the iGenomes bovine UMD3.1 genome and annotation file (chromosomes are 1,2,3) from the history. I altered the gtf file to Chr1, Chr2, Chr3… but it did not help. Another potential discrepency/conflict is that the genome and gtf file have the bosTau6 database attribute from when I uploaded them. However I am running them from the history (bosTau6 is not an option for tophat). I do not seem to be able to remove the attribute. Am I missing something else? Here is the command line Info: cufflinks v1.0.3 cufflinks -q --no-update-check -I 50000 -F 0.050000 -j 0.050000 -p 8 -G /galaxy/main_database/files/003/142/dataset_3142240.dat -N -b ref.fa Here is the details page Tool: Cufflinks Name: Cufflinks on data 69, data 4, and data 5: assembled transcripts Created: Nov 09, 2011 Filesize: 44.6 Mb Dbkey: bosTau6 Format: gtf Tool Version: Input Parameter Value SAM or BAM file of aligned RNA-Seq reads 4: Tophat for Illumina on data 4 and data 69: accepted_hits Max Intron Length 50000 Min Isoform Fraction 0.05 Pre MRNA Fraction 0.05 Perform quartile normalization Yes Conditional (reference_annotation) 1 Reference Annotation 5: iGen_UMD3_1_genes.gtf Conditional (bias_correction) 0 Conditional (seq_source) 1 Using reference file 69: UMD31_iGen_1-29X.fa Conditional (singlePaired) 0 Cordially, Chris

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Adding new data source
by Joachim Baran 12 Nov '11

12 Nov '11

Hello! I have extended a service to support asynchronous data depositing (http://wiki.g2.bx.psu.edu/Admin/Internals/Data%20Sources) but I cannot quite figure out how to access it from the Galaxy web-site. Can someone point me to the right documentation for integrating the service into Galaxy, please? I seem to be out of luck with googling today.. Thanks, Joachim

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MA2C peak calling or nimbelgen chip on chip analysis
by shamsher jagat 11 Nov '11

11 Nov '11

Do we have option of running MA2C peaks in Galaxy or is tehre an option of analyzing Chip on Chip data from Nimbelgen. Thanks

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BWA question on Mac OS X 10.7.2
by Christopher Callaway 11 Nov '11

11 Nov '11

Hi, I have tried to install BWA on my MacPro. Once installed, I typed the command make and it did not work. When installing BWA to a Linux machine, it worked fine. How do I get around this problem? Thanks, CWC

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Lastz
by Andrew South 11 Nov '11

11 Nov '11

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. 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

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my data files are missing from drop down menus
by Maya Kasowski 10 Nov '11

10 Nov '11

Hello, I uploaded a couple fastq files to Galaxy (Illumina GA2X sequencer). The files uploaded successfully and are green in the history section. However, neither file is visible in the drop down menus for any of the tools. I'd appreciate your help with this. Thank you, Maya

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Question about file formats
by Rena Zheng 10 Nov '11

10 Nov '11

Hi, I uploaded a bed file to Galaxy and did some text manipulations. I want to download the new file as a bed format that I can then open up in excel or a text editor. However, when I save the data, it is a .tabular format that I cannot open with these programs. What should I do? Thanks, Rena

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Genetrack-Indexer/PeakPredictor
by Stefanie Ververs 10 Nov '11

10 Nov '11

Hi everybody, I'm using the Genetrack-Peak-Predictor to predict nucleosome positions. I still have some questions: 1) Am I correct that the genetrack indexer seems to be down on the Public Galaxy Server? I get a server error, when I start it. (The Genetrack Browser doesn't work either; although I'm still not quite sure whether there are dependencies.) 2) By now, I know one paper on Genetrack - http://bioinformatics.oxfordjournals.org/content/24/10/1305.short and I found the following presentation slides: http://ged.msu.edu/angus/tutorials-2011/files/lecture-chipseq.pdf. Galaxy tells me to "cite Blankenberg D, et al. In preparation." Is there additional information? It would be great to know how exactly the peak predictor works, but the slides give only a kind of overview, but of course no explaining and no details and the paper isn't that clear. Thanks, Steffi/ ///

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Deleting a Galaxy User
by Oren Livne 10 Nov '11

10 Nov '11

Dear All, Is it possible to delete a galaxy user or multiple users with a UI call or an API call? Thanks, Oren

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