The ENCODE Blacklist: Identification of Problematic Regions of the Genome

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.

• NI
  National Institutes of Health

  Awards: U41 HG009293, T-32-GM007315, 1U24HG009446, GM007315
• NH
  National Human Genome Research Institute

  Awards: U41HG009293, U24HG009446
• NI
  National Institute of General Medical Sciences

  Award: T32GM007315