Fig. 1

Outline of the CHIPIN package. A Four step approach implemented in CHIPIN. B Definition of “constant genes” (red) used as a baseline for the ChIP-seq signal normalization: “constant genes” are 10% (default) of genes with the lowest standard deviation of read counts selected from different ranges of gene expression (100 bins). C Gene body regions of “constant genes” and surrounding flanking regions (± n Kb, n = 4 Kb by default) are rescaled to 40 Kb (default) and segmented into bins (default bin length: 10 bp). TSS: transcription start site; TE: transcription end site. D Main steps of the quantile normalization. In CHIPIN the quantile normalization is applied separately to subsets of genes within a certain range of ChIP-seq intensity signal (k groups, k = 20 by default). E Difference in areas under the density curves is used for the evaluation of the success of the normalization process