The ENCODE Blacklist: Identification of Problematic Regions of the Genome

Sci Rep. 2019 Jun 27;9(1):9354. doi: 10.1038/s41598-019-45839-z.


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.

Publication types

  • Research Support, N.I.H., Extramural

MeSH terms

  • Animals
  • Computational Biology / methods*
  • Databases, Genetic
  • Genome*
  • Genomics / methods*
  • Humans
  • Sequence Analysis, DNA / methods*
  • Software*