Additional file 3.

Supplementary text. Includes text on the use of MAnorm normalized read density to determine whether the peak calling cutoff is comparable between two ChIP-seq data sets; results of downstream analyses following MAnorm are robust to different peak cutoffs; integrating multiple replicates in ChIP-seq data set comparison; derivation of the P-value that quantifies the significance of differential binding at peak regions; using MAnorm to compare H3K36me3 ChIP-seq data; assessing the effect of number of common peaks used in analysis; comparing signal-to-noise ratio before and after normalization; Supplementary Methods.

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Shao et al. Genome Biology 2012 13:R16   doi:10.1186/gb-2012-13-3-r16