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, <ericliaowei@gmail.com> <ericliaowei@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!

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