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

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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Question about building a reference genome index using Bowtie
by William Light 10 Nov '11

10 Nov '11

I am trying to compare two genetically different strains that I have sequenced using SOLiD. I was trying to ask where these two strains are different, either in terms of deletions or polymorphisms, and one idea I had was to use Bowtie to create an index from one of these strains and then to map my reads for the other strain using this index. Is this a reasonable strategy? - Will Light Northwestern University

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visualization
by wu yijin 09 Nov '11

09 Nov '11

Hi All, I am new of Galaxy. I want to visualize my short mapping results in the browser. I uploaded my .wig file which has format as this, (first column is position, second is the read soverage of that position) variableStep chrom=Chr1 4 1 5 1 6 1 7 1 8 2 9 3 10 3 11 3 12 3 13 3 14 3 15 3 16 4 17 4 18 4 But it comes an error Couldn't open /galaxy/home/g2main/galaxy_main/tool-data/shared/ucsc/chrom/arabidopsis.len , No such file or directory Does anyone know how to fix this? Many thanks! Best, Peggy

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Galaxy local install problems understanding where to put mouse ref seq data to populate ref genome in BWA
by Christopher Callaway 09 Nov '11

09 Nov '11

Hello, I am still having problems understanding how to install mm9 mouse ref genome into our own install of Galaxy. When I try to map with BWA for Illumina the drop down for select ref genome is not populated with anything. How do you grab the mm9 ref file and how do you convert it so that Galaxy local "sees" it? How do you build the index and how do you prepare the loc file? Our install does not contain a folder tool-data/shared/ucsc/builds.txt. Sorry but I am not a programmer, just a bench scientist. Thanks in advance, Christopher W. Callaway University of Utah Dept. of Pediatrics Division of Neonatology 417 Wakara Way #2222 Salt Lake City, UT 84108

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TopHat/Cufflinks visualization
by Alessia D 09 Nov '11

09 Nov '11

How do people on this mailing list usually visualize Tophat and/or Cufflinks results (eg. tracks on UCSC browser)? I have only this once before, and I started with a .wig file that I uploaded to the genome browser, however it looks like Tophat does not give any .wig file in the output. Suggestions? Thanks! A

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Application error
by Palmer, Sarah 09 Nov '11

09 Nov '11

Hi, I have been trying to run fastqc on our standalone installations of Galaxy and repeatedly get the attached error message. I have tried this now with both 454 and Illumina fastq files, on 2 different Mac Machines with 10.5 and 10.6 OS and Python versions 2.5 and 2.7 on one of the machines and get the same problem occurring each time. Could you please help me find a fix for this? Cheers, Sarah

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selecting reads at random from fastq file
by Austin Paul 09 Nov '11

09 Nov '11

Hi, I am curious if anyone knows how to select random lines from a fastq file. There is a select random lines tool in text manipulation tools, but it does not treat fastq files specifically, so it will not group quality lines with sequence lines. And if I turn the fastq file to tabular form in order to select lines, I can no longer return it to fastq form. Anyone know a way to do this in galaxy? Otherwise, perhaps another program? Thanks. Austin

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