Systematic evaluation of the impact of ChIP-seq read designs on genome coverage, peak identification, and allele-specific binding detection

BMC Bioinformatics
Qi ZhangSündüz Keleş

Abstract

Chromatin immunoprecipitation followed by sequencing (ChIP-seq) experiments revolutionized genome-wide profiling of transcription factors and histone modifications. Although maturing sequencing technologies allow these experiments to be carried out with short (36-50 bps), long (75-100 bps), single-end, or paired-end reads, the impact of these read parameters on the downstream data analysis are not well understood. In this paper, we evaluate the effects of different read parameters on genome sequence alignment, coverage of different classes of genomic features, peak identification, and allele-specific binding detection. We generated 101 bps paired-end ChIP-seq data for many transcription factors from human GM12878 and MCF7 cell lines. Systematic evaluations using in silico variations of these data as well as fully simulated data, revealed complex interplay between the sequencing parameters and analysis tools, and indicated clear advantages of paired-end designs in several aspects such as alignment accuracy, peak resolution, and most notably, allele-specific binding detection. Our work elucidates the effect of design on the downstream analysis and provides insights to investigators in deciding sequencing parameters in ChIP-seq ex...Continue Reading

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Citations

Sep 24, 2020·BMC Bioinformatics·Hayato AnzawaKengo Kinoshita

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Datasets Mentioned

BETA
GM12878

Methods Mentioned

BETA
immunoprecipitation
ChIP-seq
ChIP

Software Mentioned

cnvCSEM
BWAq20o1UR
Bowtie2
Bioconductor package
AlleleSeq
ENCODE
rtracklayer
UCSC Genome Browser
CSEM
FIMO

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