The ENCODE Blacklist: Identification of Problematic Regions of the Genome

Haley M Amemiya; Anshul Kundaje; Alan P Boyle

doi:10.1038/s41598-019-45839-z

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.

Authors

Haley M Amemiya^{1

2}, Anshul Kundaje³, Alan P Boyle^{4

5

6}

Affiliations

¹ Graduate Program in Cellular and Molecular Biology, University of Michigan, Ann Arbor, MI, USA.
² Department of Computational Medicine and Bioinformatics, University of Michigan, Ann Arbor, MI, USA.
³ Department of Genetics, Stanford School of Medicine, Stanford, CA, USA. akundaje@stanford.edu.
⁴ Graduate Program in Cellular and Molecular Biology, University of Michigan, Ann Arbor, MI, USA. apboyle@umich.edu.
⁵ Department of Computational Medicine and Bioinformatics, University of Michigan, Ann Arbor, MI, USA. apboyle@umich.edu.
⁶ Department of Human Genetics, University of Michigan, Ann Arbor, MI, USA. apboyle@umich.edu.

Abstract

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*

Abstract

Publication types

MeSH terms

Grants and funding