Format

Send to

Choose Destination
See comment in PubMed Commons below
Nucleic Acids Res. 2012 Jan;40(1):e1. doi: 10.1093/nar/gkr839. Epub 2011 Oct 18.

Optimized detection of transcription factor-binding sites in ChIP-seq experiments.

Author information

1
Department of Mathematics, University of Turku, FI-20014 Turku, Finland. laliel@utu.fi

Abstract

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.

PMID:
22009681
PMCID:
PMC3245948
DOI:
10.1093/nar/gkr839
[Indexed for MEDLINE]
Free PMC Article
PubMed Commons home

PubMed Commons

0 comments
How to join PubMed Commons

    Supplemental Content

    Full text links

    Icon for Silverchair Information Systems Icon for PubMed Central
    Loading ...
    Support Center