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Old 08-19-2013, 02:50 AM   #1
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Default define if two RNA-seq samples from one individual


i have two RNA-seq libraries (~10 mio 50 PE) from tumor cells and i want to know if these are from the same person.

which is the easiest way to do this. as control i have other RNA-seq libraries from other persons...

thank you in advance,

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Old 08-19-2013, 03:17 AM   #2
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You could compare their SNPs. The number of differences due to somatic mutations should be relatively small, and you could filter out any that aren't in dbSNP. You'll also want to filter out cases where a SNP is called in one sample but not in another because the gene expression is too low. A program like SomaticSniper that directly compares two bam files might be the best way to go.
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Old 08-19-2013, 03:24 AM   #3
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If you also had independent SNP chip data then it would be a good control to compare.
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Old 08-19-2013, 11:07 PM   #4
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SomaticSniper would be the perfect answer, but unfortunately i get no results for either a same-individual pair or a different-individual pair...

the program seems to work - i get no errors - but the output-file is empty.

perhaps this program works only with exom or genomic data, not with RNA-seq data?

knows someone else a similar (easy usable) program especially for RNA-seq data. i don't want to implement a complete SNP analysis pipeline...
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