For experiments with a control, MACS linearly scales the total control tag count to be the same as the total ChIP tag count. Sometimes the same tag can be sequenced repeatedly, more times than expected from a random genome-wide tag distribution. Such tags might arise from biases during ChIP-DNA amplification and sequencing library preparation, and are likely to add noise to the final peak calls. Therefore, MACS removes duplicate tags in excess of what is warranted by the sequencing depth (binomial distribution p-value <10-5). For example, for the 3.9 million FoxA1 ChIP-Seq tags, MACS allows each genomic position to contain no more than one tag and removes all the redundancies.
