TARSII and CARSII: Two approaches for SNP-independent identification of germline differentially methylated regions in mammals

Abstract

Summary: Identifying germline differentially methylated regions (DMRs) in outbred mammals remains a challenge because of difficulty in obtaining single-nucleotide polymorphisms (SNPs). To overcome this difficulty, we developed two computational approaches, TARSII and CARSII, which allow accurate prediction of germline DMRs from DNA methylomes independent of SNPs. Furthermore, we introduce an easy and quick way to validate the predicted germline DMRs with allelic DNA methylation using CGmapTools. Collectively, our strategy can greatly facilitate de novo identification of germline DMRs in outbred mammals.For complete details on the use and execution of this protocol, please refer to Chu et al. (2021).

Keywords

• Bioinformatics
• Genomics
• Systems biology