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

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Ressource 1Download: serval:BIB_88E861A852EF.P001 (4945.34 [Ko])
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Serval ID
serval:BIB_88E861A852EF
Type
Article: article from journal or magazin.
Collection
Publications
Title
Identification and removal of low-complexity sites in allele-specific analysis of ChIP-seq data.
Journal
Bioinformatics
Author(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
Publication state
Published
Issued date
2014
Volume
30
Number
2
Pages
165-171
Language
english
Abstract
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
Yes
Create date
07/03/2014 18:54
Last modification date
25/09/2019 7:09
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