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Acetylation of histones is an important epigenetic adaptation associated with chromatin decondensation and up- or down-regulated gene expression. Chip-seq experiments targeting histone acetylation marks tend to produce coverage data that does not have the well-defined peak shapes. This can make acetylated forms of histones difficult to detect. The Histone ChIP-Seq plugin for CLC Genomics Workbench and Biomedical Genomics Workbench was specifically designed to address this problem. With minimal user guidance the tool detects evidence for histone acetylation marks in genes or other predefined genomic regions.