Shape-based peak identification for ChIP-Seq
Abstract
We present a new algorithm for the identification of bound regions from ChIP-seq experiments. Our method for identifying statistically significant peaks from read coverage is inspired by the notion of persistence in topological data analysis and provides a non-parametric approach that is robust to noise in experiments. Specifically, our method reduces the peak calling problem to the study of tree-based statistics derived from the data. We demonstrate the accuracy of our method on existing datasets, and we show that it can discover previously missed regions and can more clearly discriminate between multiple binding events. The software T-PIC (Tree shape Peak Identification for ChIP-Seq) is available at http://math.berkeley.edu/~vhower/tpic.html
Cite
@article{arxiv.1005.0793,
title = {Shape-based peak identification for ChIP-Seq},
author = {Valerie Hower and Steven N. Evans and Lior Pachter},
journal= {arXiv preprint arXiv:1005.0793},
year = {2010}
}
Comments
12 pages, 6 figures