Determine if two RNA-seq samples are repeats of each other
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6.4 years ago
kamula ▴ 10

I have 13 RNA-seq samples, all from the same condition, but with slight variations in genotype (that i believe are functionally insignificant in this condition).

How can I convince myself that I can use these 13 samples as replicates?

I've thought of using DE-Seq2 to find that there are no DE genes, but without replicates I'm not sure how much I can trust this.

rna-seq • 1.5k views
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You could do principle component analysis or look at the correlations between samples. Make sure to use between-sample normalized expression values.

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