SICER is a specialized peak caller for broad enriched histone modification (Zang, et al 2009). A comment in OMICtools also said that SICER is better than MACS for broad enrichment antibodies. However, I use MACS 1.4, the most stable version, to call H3K27me3 peaks with parameters suggested by Dr. Liu as below (Feng, et al 2012). For our ChIP-Seq data, MACS 1.4 is good enough. I used MACS, but not SICER, because we would like to use the same peak calling tool to call all ChIP-Seq data, including broad and sharp enriched peaks. In addition, MACS 2 has added broad enriched parameters (--broad) that could be helpful for your purpose.
Zang, et al. 2009. A clustering approach for identification of enriched domains from histone modification ChIP-Seq data. Bioinformatics
A comment for SICER in OMICtools
Ideal for broad peaks like H3K27me3 and H3K36me3. Where MACS will truncate peaks in smaller fragments, generating dozens of small peaks, the strenght of SICER is that you can take gaps into account. You just have to perform various tests to choose a good combination between gap size and window size. Typically, I used a window of 500nt and a gap of 3500nt for a good compromise between sensitivity and specificity.
Posted by Fabien Pichon on Oct 17, 2014
Feng JX, Liu T, Qin B, Zhang Y, Liu XS. 2012. Identifying ChIP-seq enrichment using MACS. Nature Protocols 7:1728-1740.
macs14 -t BROAD_GM12878_H3K4me3.bam -c BROAD_GM12878_H3K4me3_Control.bam -g hs -n BROAD_GM12878_H3K4me3 --nomodel --shiftsize 73 -B -S --call-subpeaks
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A. Domingues
