Genome-wide identification of positioned nucleosomes from ChIP-Seq data. (A) An example showing the workflow from sequencing tags to assigned modified nucleosomes: ChIP-Seq tags for all the available histone modifications in CD4+ T cell (shown tags for four representative marks, with arrows in each indicating its strand orientation) are combined; each tag is extended towards 3' to 150 nt (legends on the right denote tag count); taking the middle 75 nt of all the extended tags provides better signal resolution; wavelet denoising smoothes the signal; LoG identifies peaks as positioned nucleosomes; histone modifications are assigned to individual identified nucleosomes. (B) Examples of peaks with unbalanced tag counts. Narrow regions A and B were repeatedly sequenced, creating the four flanking peaks with unbalanced tag counts between plus (pink) and minus (blue) strands as shown in the pie charts. They might arise from repetitive sequences in unsequenced or unannotated genome regions, thus were removed from further analysis.