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  • cross correlation for paired-end ChIP-seq

    Would this still be a useful tool to assess ChIP quality? If I understand correctly, this is used for single end experiments because it is necessary to estimate the fragment size (but unnecessary since paired-end data gives you exact fragment size).

    Has anyone computed this anyway with paired-end data as a measure for how well your IP worked? If so, would simply using either R1 or R2 of each pair be a reasonable approach?

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