MESIA: multi-epigenome sample integration approach for precise peak calling

Abstract

The assay for transposase-accessible chromatin with sequencing (ATAC-seq) is the most widely used method for measuring chromatin accessibility. Researchers have included multi-sample replication in ATAC-seq experimental designs. In epigenomic analysis, researchers should measure subtle changes in the peak by considering the read depth of individual samples. It is important to determine whether the peaks of each replication have an integrative meaning for the region of interest observed during multi-sample integration. We developed multi-epigenome sample integration approach for precise peak calling (MESIA), which integrates replication with high representativeness and reproducibility in multi-sample replication and determines the optimal peak. After identifying the reproducibility between all replications, our method integrated multiple samples determined as representative replicates. MESIA detected 6.06 times more peaks, and the value of the peaks was 1.32 times higher than the previously used method. MESIA is a shell-script-based open-source code that provides researchers involved in the epigenome with comprehensive insights.