The composite blacklist is made up of several components. It has the lifted mm9 blacklist from Anshul, the mitochondrial blacklist regions from Peng (Wold lab), and the blacklist regions from Penn State.
The blacklist regions from Penn State are from the input signal. It is comprised of peaks called by Macs on the input signal, and windows with with a high signal. The high signal is defined by a 5,000 base pair sliding window with an average signal 4 fold greater than the genome average and a maximum score of at least 8 fold greater. The composite track has a union of all the cell specific blacklist regions. This was computed on the mm10 reference sequence that includes unplaced scaffolds, but not alternate chromosomes.
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