A1 Vertaisarvioitu alkuperäisartikkeli tieteellisessä lehdessä
Optimizing Detection of Transcription Factor-Binding Sites in ChIP-seq Experiments
Tekijät: Elo LL, Kallio A, Laajala TD, Hawkins RD, Korpelainen E, Aittokallio T
Toimittaja: Noam Shomron
Kustantaja: OXFORD UNIV PRESS
Julkaisuvuosi: 2012
Journal: Nucleic Acids Research
Kokoomateoksen nimi: Deep Sequencing Data Analysis
Tietokannassa oleva lehden nimi: NUCLEIC ACIDS RESEARCH
Lehden akronyymi: NUCLEIC ACIDS RES
Artikkelin numero: ARTN e1
Numero sarjassa: 1
Vuosikerta: 40
Numero: 1
Sivujen määrä: 11
ISBN: 978-1-62703-513-2
ISSN: 0305-1048
DOI: https://doi.org/10.1093/nar/gkr839
Tiivistelmä
We developed a computational procedure for optimizing the binding site detections in a given ChIP-seq experiment by maximizing their reproducibility under bootstrap sampling. We demonstrate how the procedure can improve the detection accuracies beyond those obtained with the default settings of popular peak calling software, or inform the user whether the peak detection results are compromised, circumventing the need for arbitrary re-iterative peak calling under varying parameter settings. The generic, open-source implementation is easily extendable to accommodate additional features and to promote its widespread application in future ChIP-seq studies. The peakROTS R-package and user guide are freely available at http://www.nic.funet.fi/pub/sci/molbio/peakROTS.
We developed a computational procedure for optimizing the binding site detections in a given ChIP-seq experiment by maximizing their reproducibility under bootstrap sampling. We demonstrate how the procedure can improve the detection accuracies beyond those obtained with the default settings of popular peak calling software, or inform the user whether the peak detection results are compromised, circumventing the need for arbitrary re-iterative peak calling under varying parameter settings. The generic, open-source implementation is easily extendable to accommodate additional features and to promote its widespread application in future ChIP-seq studies. The peakROTS R-package and user guide are freely available at http://www.nic.funet.fi/pub/sci/molbio/peakROTS.
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