Identification of blacklist regions in cattle and pig genomes

Cattle and pigs are important farm animals and biomedical models for studying human development and diseases. Accurate annotation of their cis-regulatory elements is essential for advancing breeding strategies and biological research. Identifying these elements typically relies on ChIP-seq data, which profiles histone modifications and transcription factors. Although some large-scale ChIP-seq projects have decoded functional genomes in cattle and pigs, no comprehensive blacklist identification has been performed. In this study, we systematically identified and evaluated blacklist regions in cattle and pig genomes using the ENCODE pipeline. We annotated 126.8 Mb and 99.9 Mb of blacklist regions in cattle and pigs, respectively. We found that removing these blacklist regions is a critical quality control measure that can enhance the reliability of ChIP-seq analysis. Overall, our results provide a valuable resource for farm animal research, and we propose eliminating these problematic regions to reduce abnormally high signals and improve downstream analyses.