Identification and removal of low-complexity sites in allele-specific analysis of ChIP-seq data

Waszak, Sebastian M; Kilpinen, Leena Helena; Gschwind, Andreas R; Orioli, Andrea; Raghav, Sunil K; Witwicki, Robert M; Migliavacca, Eugenia; Yurovsky, Alisa; Lappalainen, Tuuli Emilia; Hernandez, Nouria; Reymond, Alexandre; Dermitzakis, Emmanouil; Deplancke, Bart

doi:10.1093/bioinformatics/btt667

Scientific article

English

Identification and removal of low-complexity sites in allele-specific analysis of ChIP-seq data

ContributorsWaszak, Sebastian M; Kilpinen, Leena Helena; Gschwind, Andreas R; Orioli, Andrea; Raghav, Sunil K; Witwicki, Robert M; Migliavacca, Eugenia; Yurovsky, Alisa; Lappalainen, Tuuli Emilia; Hernandez, Nouria; Reymond, Alexandre; Dermitzakis, Emmanouil; Deplancke, Bart

Published inBioinformatics, vol. 30, no. 2, p. 165-171

Publication date2014

Abstract

High-throughput sequencing technologies enable the genome-wide analysis of the impact of genetic variation on molecular phenotypes at unprecedented resolution. However, although powerful, these technologies can also introduce unexpected artifacts.

Keywords

Alleles
Binding Sites
Chromatin Immunoprecipitation/methods
Female
Gene Library
Genome, Human
Humans
Lymphocytes/cytology/metabolism
Male
Oligonucleotide Array Sequence Analysis/methods
Polymorphism, Single Nucleotide/genetics
RNA Polymerase II/genetics

Affiliation entities

Faculté de médecine / Section de médecine fondamentale / Département de médecine génétique et développement

Research groups

Population Genomics and Genetics of Complex Traits (892)

Citation (ISO format)

WASZAK, Sebastian M et al. Identification and removal of low-complexity sites in allele-specific analysis of ChIP-seq data. In: Bioinformatics, 2014, vol. 30, n° 2, p. 165–171. doi: 10.1093/bioinformatics/btt667

Article (Published version)

Identifiers

PID : unige:90277
DOI : 10.1093/bioinformatics/btt667
PMID : 24255646

Journal ISSN1367-4803

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Identification and removal of low-complexity sites in allele-specific analysis of ChIP-seq data

High-throughput sequencing technologies enable the genome-wide analysis of the impact of genetic variation on molecular phenotypes at unprecedented resolution. However, although powerful, these technologies can also introduce unexpected artifacts.

Technical informations