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

ABSTRACT:

Summary

Exclusion regions are sections of reference genomes with abnormal pileups of short sequencing reads. Removing reads overlapping them improves biological signal, and these benefits are most pronounced in differential analysis settings. Several labs created exclusion region sets, available primarily through ENCODE and Github. However, the variety of exclusion sets creates uncertainty which sets to use. Furthermore, gap regions (e.g. centromeres, telomeres, short arms) create additional considerations in generating exclusion sets. We generated exclusion sets for the latest human T2T-CHM13 and mouse GRCm39 genomes and systematically assembled and annotated these and other sets in the excluderanges R/Bioconductor data package, also accessible via the BEDbase.org API. The package

SUBMITTER: Ogata JD 

PROVIDER: S-EPMC10126321 | biostudies-literature | 2023 Apr

REPOSITORIES: biostudies-literature