Normalization of ChIP-seq data with control.

ABSTRACT:

Background

ChIP-seq has become an important tool for identifying genome-wide protein-DNA interactions, including transcription factor binding and histone modifications. In ChIP-seq experiments, ChIP samples are usually coupled with their matching control samples. Proper normalization between the ChIP and control samples is an essential aspect of ChIP-seq data analysis.

Results

We have developed a novel method for estimating the normalization factor between the ChIP and the control samples. Our method, named as NCIS (Normalization of ChIP-seq) can accommodate both low and high sequencing depth datasets. We compare statistical properties of NCIS against existing methods in a set of diverse simulation settings, where NCIS enjoys the best estimation precision. In addition, we il

SUBMITTER: Liang K 

PROVIDER: S-EPMC3475056 | biostudies-literature | 2012 Aug

REPOSITORIES: biostudies-literature