Nucleic Acids Research Advance Access published online on November 11, 2009
Nucleic Acids Research, doi:10.1093/nar/gkp1012
Methods Online |
Sole-Search: an integrated analysis program for peak detection and functional annotation using ChIP-seq data
1Genome Center, 2Department of Computer Science, 3Department of Molecular and Cellular Biology and 4Department of Pharmacology, University of California-Davis, Davis, CA 95616, USA
*To whom correspondence should be addressed. Tel: +1 530 754 4988; Fax: +1 530 754 9658; Email: pjfarnham{at}ucdavis.edu
Received August 10, 2009. Revised September 29, 2009. Accepted October 19, 2009.
Next-generation sequencing is revolutionizing the identification of transcription factor binding sites throughout the human genome. However, the bioinformatics analysis of large datasets collected using chromatin immunoprecipitation and high-throughput sequencing is often a roadblock that impedes researchers in their attempts to gain biological insights from their experiments. We have developed integrated peak-calling and analysis software (Sole-Search) which is available through a user-friendly interface and (i) converts raw data into a format for visualization on a genome browser, (ii) outputs ranked peak locations using a statistically based method that overcomes the significant problem of false positives, (iii) identifies the gene nearest to each peak, (iv) classifies the location of each peak relative to gene structure, (v) provides information such as the number of binding sites per chromosome and per gene and (vi) allows the user to determine overlap between two different experiments. In addition, the program performs an analysis of amplified and deleted regions of the input genome. This software is web-based and automated, allowing easy and immediate access to all investigators. We demonstrate the utility of our software by collecting, analyzing and comparing ChIP-seq data for six different human transcription factors/cell line combinations.