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comparing NGS tracks

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I am comparing the output of two chromatin profiling methods.

So far I mapped my reads to the genome and compared the resulting bed files by using bedtools jaccard.

However, as the data in one track is rather noisy I fear that the bedtools jaccard score (calculated via overlapp) does not necessary represent the real, significant sample similarity. So is it advisable to perform peak calling before comparing?

I was also wondering if there is a "gold standard" for comparing two different ngs tracks?
asked Apr 8, 2015 in NGS data analysis by falko.hofmann (400 points)
recategorized Apr 8, 2015 by falko.hofmann

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