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Functional genomics assays based on high-throughput sequencing greatly expand our ability to understand the genome. Here, we define the ENCODE blacklist- a comprehensive set of regions in the human, mouse, worm, and fly genomes that have anomalous, unstructured, or high signal in next-generation sequencing experiments independent of cell line or experiment. The removal of the ENCODE blacklist is an essential quality measure when analyzing functional genomics data.
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Amemiya, H. M., Kundaje, A. B., & Boyle, A. P. (2019). The ENCODE Blacklist: Identification of Problematic Regions of the Genome. Scientific Reports, 9(1), 9354–9354. https://doi.org/10.1038/s41598-019-45839-z
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