The ENCODE Blacklist: Identification of Problematic Regions of the Genome
By Haley M. Amemiya, Anshul B Kundaje, Alan P. Boyle. Scientific Reports, 2019
1,583 citations recorded by the source corpus.
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.
Subfields: Molecular Biology
View Paper: https://www.semanticscholar.org/paper/e4d9a4ecd457b234989d692741f30dea20ea7293
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In Molecular Biology
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Citations in the corpus
- Genome-wide enhancer maps link risk variants to disease genes (2021, methodology): “To this list we added 500 bp regions centred on all gene TSS’s and removed any peaks overlapping blacklisted regions (version 1 from https://sites.google.com/site/anshulkundaje/projects/blacklists) 8,48 .”
- The design and construction of reference pangenome graphs with minigraph (2020, methodology): “We constructed a human pangenome graph excluding CHM1 and CHM13, the two samples used in the SynDip benchmark [4], and generated regions around variations (see Methods), which we call as blacklist regions, following the rationale in [45].”
- Assessment of computational methods for the analysis of single-cell ATAC-seq data (2019, methodology): “830 cisTopic, Scasat, SCRAT, and SnapATAC employ a blacklist filtering step to remove 831 features annotated by ENCODE as belonging to a subset of genomic regions, which 832 harbor the potential to produce artifacts in downstream analysis steps [24].”
- ArchR is a scalable software package for integrative single-cell chromatin accessibility analysis (2021, background): “Blacklisted regions, regions that have “anomalous, unstructured, or high signal in next-generation sequencing experiments independent of cell line or experiment” 49 , are excluded from this tile matrix.”