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

Détails

ID Serval
serval:BIB_88E861A852EF
Type
Article: article d'un périodique ou d'un magazine.
Collection
Publications
Titre
Identification and removal of low-complexity sites in allele-specific analysis of ChIP-seq data.
Périodique
Bioinformatics
Auteur(s)
Waszak S.M., Kilpinen H., Gschwind A.R., Orioli A., Raghav S.K., Witwicki R.M., Migliavacca E., Yurovsky A., Lappalainen T., Hernandez N., Reymond A., Dermitzakis E.T., Deplancke B.
ISSN
1367-4811 (Electronic)
ISSN-L
1367-4803
Statut éditorial
Publié
Date de publication
2014
Volume
30
Numéro
2
Pages
165-171
Langue
anglais
Résumé
MOTIVATION: 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. Results: We investigated the impact of library amplification bias on the identification of allele-specific (AS) molecular events from high-throughput sequencing data derived from chromatin immunoprecipitation assays (ChIP-seq). Putative AS DNA binding activity for RNA polymerase II was determined using ChIP-seq data derived from lymphoblastoid cell lines of two parent-daughter trios. We found that, at high-sequencing depth, many significant AS binding sites suffered from an amplification bias, as evidenced by a larger number of clonal reads representing one of the two alleles. To alleviate this bias, we devised an amplification bias detection strategy, which filters out sites with low read complexity and sites featuring a significant excess of clonal reads. This method will be useful for AS analyses involving ChIP-seq and other functional sequencing assays.
Pubmed
Web of science
Open Access
Oui
Création de la notice
07/03/2014 18:54
Dernière modification de la notice
20/08/2019 15:48
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