Is this the right normalization? A diagnostic tool for ChIP-seq normalization

Quantifying ChIP-seq data: a spiking method providing an internal reference for sample-to-sample normalization.

Chromatin immunoprecipitation followed by deep sequencing (ChIP-seq) experiments are widely used to determine, within entire genomes, the occupancy sites of any protein of interest, including, for example, transcription factors, RNA polymerases, or histones with or without various modifications. In addition to allowing the determination of occupancy sites within one cell type and under one cond...

Supplement Materials for Normalization of ChIP - seq data with control Kun

We demonstrate that a proper control sample correlates linearly with the background parts of its corresponding ChIP sample. In the following examples, we first draw the original ChIP vs control bins counts to show the over-abundance of high ChIP count bins due to binding signals. Then we filter the strong binding signals by calling peaks with SPP (Kharchenko et al., 2008) at FDR 0.1 level and e...

miRNA-Seq normalization comparisons need improvement.

cDNA Microarray Data Normalization

Comparative study on ChIP-seq data: normalization and binding pattern characterization

MOTIVATION Antibody-based Chromatin Immunoprecipitation assay followed by high-throughput sequencing technology (ChIP-seq) is a relatively new method to study the binding patterns of specific protein molecules over the entire genome. ChIP-seq technology allows scientist to get more comprehensive results in shorter time. Here, we present a non-linear normalization algorithm and a mixture modelin...