The ENCODE Blacklist: Identification of Problematic Regions of the Genome
Open accessAbstract
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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Peaks in ENCODE blacklisted regions were removed using the intersect function in bedtools2.
“Peaks in ENCODE blacklisted regions (95) were removed using the intersect function in bedtools2 (96) v2.30.0.”
From Synergy between regulatory elements can render cohesin dispensable for distal enhancer function (2026) · cites this paper as [95]
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The Sequence Alignment/Map format and SAMtools
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Research works printed but not linked: 9
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InfluentialAn extended transcription factor regulatory network controls hepatocyte identity
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- Authors
- Amemiya, H. M., Kundaje, A., & Boyle, A. P.
- Affiliations
- University of Michigan (US)
- Stanford Medicine (US)
- Corresponding author
- Kundaje, Anshul
- Boyle, Alan P.
- Venue
- Scientific Reports
- Published
- 2019-06-27
- Volume
- 9
- Issue
- 1
- Pages
- 9354-9354
- ISSN
- 2045-2322 (ISSN-L)
- PMC
- PMC6597582
- OpenAlex
- W2953622121
- Cited by
- 1,831
- References
- 1
- Citations by year
- 2026: 259 · 2025: 367 · 2024: 334 · 2023: 316 · 2022: 236 · 2021: 195 · 2020: 107 · 2019: 16 · 2012: 1
- FWCI
- 46.14
- Type
- journal article
- Language
- en
- Open access
- gold
- doi.org
- Locations
- Scientific Reports (publishedVersion, cc-by)
- PubMed Central (publishedVersion, cc-by)
- PubMed (publishedVersion)
- DOAJ (DOAJ: Directory of Open Access Journals) (submittedVersion)
- Funders
- U.S. Department of Health & Human Services | NIH | National Institute of General Medical Sciences (T32GM007315)
- U.S. Department of Health & Human Services | NIH | National Human Genome Research Institute (U24HG009446, U41HG009293)
- Topics
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › Genomics and Chromatin Dynamics
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › Genomics and Phylogenetic Studies
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › Bioinformatics and Genomic Networks
- Keywords
- sequencing artifacts, human genome, mouse genome, Caenorhabditis elegans genome, Drosophila genome
- MeSH terms
- Animals, Humans, Software, Genome, Sequence Analysis, DNA, Computational Biology, Genomics, Databases, Genetic
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