ChIPbinner: an R package for analyzing broad histone marks binned in uniform windows from ChIP-Seq or CUT&RUN/TAG data

Table 1 Normalizing solely by library size outperformed edgeR normalization in true positive detection for simulated ChIP-Seq data

Histone mark	Normalization	# of true downregulated bins	Ratio of detected downregulated bins (library size/edgeR)
H3K36me2	Library size	8071	2.7
H3K36me2	edgeR	3072	2.7
H3K4me1	Library size	6469	1.7
H3K4me1	edgeR	3810	1.7
H3K27me3	Library size	4358	7.0
H3K27me3	edgeR	621	7.0
H3K9me3	Library size	5689	5.5
H3K9me3	edgeR	1027	5.5

50,000 10 kb-bins were randomly sampled for each histone mark. For both normalization methods, ROTS differential analysis was used to identify downregulated (FDR < 0.05 & logFC < 0) & upregulated (FDR < 0.05 & logFC > 0) bins

ISSN: 1471-2105