Dear sir, I was looking through your Galaxy Wiki, but could not find an answer to my question. I would most appreciate any help regarding the following issue: I'm conducting a GWAS study in horses. Up until now I've been using PLINK for my association analysis, and now I wish to generate a Manhattan plot. I've been looking through your online version of Galaxy-Tool under SNP/WGA: QC; LD; Plots <http://main.g2.bx.psu.edu/root/tool_menu#> --> Manhattan/QQ:<http://main.g2.bx.psu.edu/tool_runner?tool_id=rgManQQ1> link, and I've read all the instructions. I think I have an appropriate file ready to run this on your online version, but I was hoping you can send me an example file of how exactly the data should look like (and not just brief explanations about the syntax), and in what format exactly should I upload it? If you have a tutorial about this, even better. Many thanks! Sincerely, Sagi Polani Molecular Evolution Lab Koret School of Veterinary Medicine The Hebrew University of Jerusalem Israel
As the tool help says about the input file: "Tabular Data is a tab delimited header file with chromosome, offset and p values to be plotted" In other words if you have a text file containing tab delimited columns, with a header row and some data you should be good to go. Attached is a sample that works for me on main - although the plots look rather silly. On Sun, Jun 19, 2011 at 6:53 PM, Sagi <sagi.polani@gmail.com> wrote:
Dear sir, I was looking through your Galaxy Wiki, but could not find an answer to my question. I would most appreciate any help regarding the following issue: I'm conducting a GWAS study in horses. Up until now I've been using PLINK for my association analysis, and now I wish to generate a Manhattan plot. I've been looking through your online version of Galaxy-Tool under SNP/WGA: QC; LD; Plots --> Manhattan/QQ: link, and I've read all the instructions. I think I have an appropriate file ready to run this on your online version, but I was hoping you can send me an example file of how exactly the data should look like (and not just brief explanations about the syntax), and in what format exactly should I upload it? If you have a tutorial about this, even better. Many thanks! Sincerely, Sagi Polani Molecular Evolution Lab Koret School of Veterinary Medicine The Hebrew University of Jerusalem Israel
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-- Ross Lazarus MBBS MPH; Associate Professor, Harvard Medical School; Director of Bioinformatics, Channing Lab; Tel: +1 617 505 4850; Head, Medical Bioinformatics, BakerIDI; Tel: +61 385321444;
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