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nservant / HiC-Pro

HiC-Pro: An optimized and flexible pipeline for Hi-C data processing
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m #505

Open BenxiaHu opened 2 years ago

nservant commented 2 years ago

Hello 1: Not sure what you mean ? The goal of the iced normalization is to normalize each row/column of your matrix to a constant (usually =1). In the case of HiC-Pro, this constant is fixed to the mean of contact values, so indeed, it does not correct for sequencing depth 2: The iced normalization is run on the entire genome, not per chromosome Best

nservant commented 2 years ago

1: by normalize, I mean ICED normalized or balanced if you wish. Not sure to understand your question ? 2: The ICED balancing algorithm is run on a genome-wide matrix, that's it.