HI,

I have RNA-Seq data from cancer tumor sample and two reference normal sample and I want to find out SNPs and mutations in my data and the only available sources for me to do analysis is the Galaxy.

I did the alignment using tophat, ran pileup on tophats output .bam files for all the four samples following with filter pileup.

My main question is how to find SNPs in tumor sample compared to its normal sample.

Can anyone show a step-by-step procedure of how to find SNPs in Galaxy.

Thanks in advance