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how to identify if RNAseq data is from same patient

HI all,

I have RNAseq data from the same pateint before and after treatment. If I had to check if they are the same individual- how do i do this based on RNAseq data. Call variants and see? Please suggest of any ways of doing it.

Thanks, mamta

rnaseq variants
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updated by John John • written by datanerd datanerd

2 answers

Don't call the SNP genome-widely, since there will be large number sudo-SNPs caused by RNA-edit. What you need to do it check the status of the 100,000 classic high frequent SNPs (Download it from UCSC) and then you can do the cluster analysis. I think it is power enough to identify the same individual.

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written by Shicheng Guo Shicheng Guo

Thanks Shicheng. I will try doing that. Any specific program that you could suggest to call variants?

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written by datanerd datanerd

Depending on your depth, GATK is probably your best bet

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written by andrew.j.skelton73 andrew.j.skelton73

You probably thought of this already, but if one sample has a Y chromosome and one does not, thats a pretty big give-away.

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written by John John

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