excluderanges: exclusion sets for T2T-CHM13, GRCm39, and other genome assemblies

• DOI: 10.1093/bioinformatics/btad198
• Publication Date: 2023-04-17T14:25:58Z
• Authors: Jonathan D Ogata; Wancen Mu; Eric S Davis; Bingjie Xue; J Chuck Harrell; Nathan C Sheffield; Douglas H Phanstiel; Michael I Love; Mikhail G Dozmorov
• Keywords: Bioconductor; Blacklist; ENCODE

Abstract Summary Exclusion regions are sections of reference genomes with abnormal pileups short sequencing reads. Removing reads overlapping them improves biological signal, and these benefits most pronounced in differential analysis settings. Several labs created exclusion region sets, available primarily through ENCODE Github. However, the variety sets creates uncertainty which to use. Furthermore, gap (e.g. centromeres, telomeres, arms) create additional considerations generating sets. We generated for latest human T2T-CHM13 mouse GRCm39 systematically assembled annotated other excluderanges R/Bioconductor data package, also accessible via BEDbase.org API. The package provides unified access 82 GenomicRanges objects covering six organisms, multiple genome assemblies, types regions. For hg38 assembly, we recommend hg38.Kundaje.GRCh38_unified_blacklist as well-curated annotated, by Blacklist tool organisms. Availability implementation https://bioconductor.org/packages/excluderanges/. Package website: https://dozmorovlab.github.io/excluderanges/.