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.
Keywords
BlacklistENCODEGenomeGenomicsComputational biologyIdentification (biology)BiologyDNA sequencingHuman genomeFunctional genomicsGeneticsComputer scienceGeneWorld Wide Web
MeSH Terms
AnimalsComputational BiologyDatabasesGeneticGenomeGenomicsHumansSequence AnalysisDNASoftware
Affiliated Institutions
Related Publications
Single-cell transcriptome sequencing: recent advances and remaining challenges
<ns4:p>Single-cell RNA-sequencing methods are now robust and economically practical and are becoming a powerful tool for high-throughput, high-resolution transcriptomic analysis...
Comparative Genomics of the Eukaryotes
A comparative analysis of the genomes of Drosophila melanogaster , Caenorhabditis elegans , and Saccharomyces cerevisiae —and the proteins they are predicted to encode—was under...
ENCODE whole-genome data in the UCSC Genome Browser: update 2012
The Encyclopedia of DNA Elements (ENCODE) Consortium is entering its 5th year of production-level effort generating high-quality whole-genome functional annotations of the human...
Reliable prediction of regulator targets using 12 <i>Drosophila</i> genomes
Gene expression is regulated pre- and post-transcriptionally via cis -regulatory DNA and RNA motifs. Identification of individual functional instances of such motifs in genome s...
RNA-seq: An assessment of technical reproducibility and comparison with gene expression arrays
Ultra-high-throughput sequencing is emerging as an attractive alternative to microarrays for genotyping, analysis of methylation patterns, and identification of transcription fa...
Publication Info
- Year
- 2019
- Type
- article
- Volume
- 9
- Issue
- 1
- Pages
- 9354-9354
- Citations
- 1883
- Access
- Closed
External Links
Social Impact
Altmetric
PlumX Metrics
Social media, news, blog, policy document mentions
Citation Metrics
1883
OpenAlex
75
Influential
Cite This
Haley M. Amemiya,
Anshul Kundaje,
Alan P. Boyle
(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
Identifiers
- DOI
- 10.1038/s41598-019-45839-z
- PMID
- 31249361
- PMCID
- PMC6597582