Wei, The pileup tool will help you find SNPs in your data; you'll want to read the documentation to understand how best to use it for your needs. You can also try the Unified Genotyper on our test server ( http://test.g2.bx.psu.edu/ ), but it's in alpha/beta status and we aren't providing any support for it yet.
Good luck, J. On Jan 9, 2012, at 1:28 AM, <ericliao...@gmail.com> <ericliao...@gmail.com> wrote: > HI, > I am new to the RNA-seq, and the only available sources for me to do analysis > is the Galaxy server. I want find out SNP and point mutations in RNA-Seq data > using Galaxy (I do not know if anyone using RNA-seq data to find point > mutations, because there is whole Genome sequencing for reporting mutations > and SNPs). I have been searching in the forum for a step-by-step protocols > for doing it, but could not find it. > I have one normal sample and two cancer samples, a TopHat produced "accepted > Hits.bam" file for each one. > I want to find out SNP and point mutations in the cancer samples, so How do I > go from here? Can anyone show me how to do it in Galaxy main server? > Thanks! > > Wei > ___________________________________________________________ > 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/
___________________________________________________________ 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/
