Normalization of ChIP-seq data with control
نویسندگان
چکیده
منابع مشابه
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...
متن کاملQuantifying 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...
متن کاملComparative 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...
متن کاملComputational analysis of ChIP-seq data.
Chromatin immunoprecipitation followed by massively parallel sequencing (ChIP-seq) is a new technology to map protein-DNA interactions in a genome. The genome-wide transcription factor binding site and chromatin modification data produced by ChIP-seq provide invaluable information for studying gene regulation. This chapter reviews basic characteristics of ChIP-seq data and introduces a computat...
متن کاملHierarchical hidden Markov model with application to joint analysis of ChIP-chip and ChIP-seq data
MOTIVATION Chromatin immunoprecipitation (ChIP) experiments followed by array hybridization, or ChIP-chip, is a powerful approach for identifying transcription factor binding sites (TFBS) and has been widely used. Recently, massively parallel sequencing coupled with ChIP experiments (ChIP-seq) has been increasingly used as an alternative to ChIP-chip, offering cost-effective genome-wide coverag...
متن کاملذخیره در منابع من
با ذخیره ی این منبع در منابع من، دسترسی به آن را برای استفاده های بعدی آسان تر کنید
ژورنال
عنوان ژورنال: BMC Bioinformatics
سال: 2012
ISSN: 1471-2105
DOI: 10.1186/1471-2105-13-199