Re: [galaxy-user] SNP finding
Dear Galaxy UsersI wondered if anybody is having the same problem.I am trying to run CuffDiff using the latest version of GenCode18 and keep getting the following error message.Is there a problem with the network or is it me?Best wishesMark___ 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/ To search Galaxy mailing lists use the unified search at: http://galaxyproject.org/search/mailinglists/
Re: [galaxy-user] SNP finding
Hello Xiefan, This page has a simple breakdown of how to call variants within Galaxy. This is brand new, so full annotation/video is pending, but it should still be straightforward to see how the data is prepped and which tools are used. https://usegalaxy.org/u/galaxyproject/p/galaxy-101-ngs-variant Another set of tutorial videos cover the tools, which you can use on the public site or on a scaled up cloud server as needed: https://vimeo.com/channels/galaxytoolshed Hopefully this help you to get started. Jen Galaxy team On 10/21/12 3:11 PM, Xiefan Fang wrote: Dear galaxy users, We have done deep sequencing on some known genomic loci using Hiseq2000. I have already mapped the reads to the reference sequences by using Galaxy. In the next step, I want to find SNPs and calculate the SNP percentage within the reads. There are 500,000 to 1,000,000 reads per biological sample. Can I do it with galaxy? If not, is there other programs available in windows? Considering that I am not very familiar with programming. Thanks, Xiefan University of Florida ___ 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/ -- Jennifer Hillman-Jackson http://galaxyproject.org ___ 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/ To search Galaxy mailing lists use the unified search at: http://galaxyproject.org/search/mailinglists/
Re: [galaxy-user] SNP finding
Hi Mark, This error is not tool related. Could you click the “bug” icon to send us an error report? —nate On Nov 11, 2013, at 8:33 AM, Mark Lindsay m.a.lind...@bath.ac.uk wrote: Dear Galaxy Users I wondered if anybody is having the same problem. I am trying to run CuffDiff using the latest version of GenCode18 and keep getting the following error message. Is there a problem with the network or is it me? Best wishes Mark Screen Shot 2013-11-11 at 13.32.12.png ___ 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/ To search Galaxy mailing lists use the unified search at: http://galaxyproject.org/search/mailinglists/ ___ 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/ To search Galaxy mailing lists use the unified search at: http://galaxyproject.org/search/mailinglists/
