ChIP-seq analysis algorithms are specialized in identifying one of two types of enrichment (or have specific methods for each): broad peaks or broad domains (i.e. histone modifications that cover entire gene bodies) or narrow peaks (i.e. a transcription factor binding).
- 一种是broad peaks：整个基因范围内都存在组蛋白修饰，因此峰较多，较分散
- 一种是narrow peaks：转录因子结合
Narrow peaks are easier to detect as we are looking for regions that have higher amplitude and are easier to distinguish from the background, compared to broad or dispersed marks
Model-based Analysis of ChIP-seq (MACS) 有三种模式：broad、narrow、mixed（mix模式适用于不易判断的类型，比如PolII的结合存在于启动子和跨越基因长度，broad和narrow并存）
ENCODE的broad peaks、narrow peaks
- H3K9me3 is an exception as it is enriched in repetitive regions of the genome. Compared to other broad marks, there are few H3K9me3 peaks in non-repetitive regions of the genome in tissues and primary cells. This results in many ChIP-seq reads that map to a non-unique position in the genome. Tissues and primary cells should have 45 million total mapped reads per replicate.