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? 

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