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Old 12-14-2012, 10:01 AM   #1
suz.katie
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Location: Virginia

Join Date: Dec 2012
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Default Find out SNPs and Mutations in RNA-Seq data

HI,
I am new to the RNA-seq and the only available sources for me to do analysis
is the Galaxy server. 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.

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
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galaxy, rna seq, snp analysis

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