dc.contributor.author
Hansen, Peter
dc.contributor.author
Hecht, Jochen
dc.contributor.author
Ibn-Salem, Jonas
dc.contributor.author
Menkuec, Benjamin S.
dc.contributor.author
Roskosch, Sebastian
dc.contributor.author
Truss, Matthias
dc.contributor.author
Robinson, Peter N.
dc.date.accessioned
2018-06-08T10:33:55Z
dc.date.available
2016-12-22T12:22:52.697Z
dc.identifier.uri
https://refubium.fu-berlin.de/handle/fub188/20668
dc.identifier.uri
http://dx.doi.org/10.17169/refubium-23968
dc.description.abstract
Background ChIP-nexus, an extension of the ChIP-exo protocol, can be used to
map the borders of protein-bound DNA sequences at nucleotide resolution,
requires less input DNA and enables selective PCR duplicate removal using
random barcodes. However, the use of random barcodes requires additional
preprocessing of the mapping data, which complicates the computational
analysis. To date, only a very limited number of software packages are
available for the analysis of ChIP-exo data, which have not yet been
systematically tested and compared on ChIP-nexus data. Results Here, we
present a comprehensive software package for ChIP-nexus data that exploits the
random barcodes for selective removal of PCR duplicates and for quality
control. Furthermore, we developed bespoke methods to estimate the width of
the protected region resulting from protein-DNA binding and to infer binding
positions from ChIP-nexus data. Finally, we applied our peak calling method as
well as the two other methods MACE and MACS2 to the available ChIP-nexus data.
Conclusions The Q-nexus software is efficient and easy to use. Novel
statistics about duplication rates in consideration of random barcodes are
calculated. Our method for the estimation of the width of the protected region
yields unbiased signatures that are highly reproducible for biological
replicates and at the same time very specific for the respective factors
analyzed. As judged by the irreproducible discovery rate (IDR), our peak
calling algorithm shows a substantially better reproducibility. An
implementation of Q-nexus is available at http://charite.github.io/Q/.
en
dc.rights.uri
http://creativecommons.org/licenses/by/4.0/
dc.subject
Chromatin immunoprecipitation
dc.subject
Duplication rates
dc.subject
Library complexity
dc.subject
Bioinformatics
dc.subject.ddc
600 Technik, Medizin, angewandte Wissenschaften::610 Medizin und Gesundheit
dc.type
Wissenschaftlicher Artikel
dcterms.bibliographicCitation
BMC Genomics. - 17 (2016), Artikel Nr. 873
dc.title.subtitle
a comprehensive and efficient analysis pipeline designed for ChIP-nexus
dcterms.bibliographicCitation.doi
10.1186/s12864-016-3164-6
dcterms.bibliographicCitation.url
http://bmcgenomics.biomedcentral.com/articles/10.1186/s12864-016-3164-6
refubium.affiliation
Charité - Universitätsmedizin Berlin
de
refubium.mycore.fudocsId
FUDOCS_document_000000026069
refubium.note.author
Der Artikel wurde in einer reinen Open-Access-Zeitschrift publiziert.
refubium.resourceType.isindependentpub
no
refubium.mycore.derivateId
FUDOCS_derivate_000000007464
dcterms.accessRights.openaire
open access