CGR

Abstract

ChIP-seq, which combines chromatin immunoprecipitation with massively parallel short-read sequencing, can profile in vivo genome-wide transcription factor-DNA association with higher sensitivity, specificity and spatial resolution than ChIP- chip. While it presents new opportunities for research, ChIP-seq poses new challenges for statistical analysis that derive from the complexity of the biological systems characterized and the variability and biases in its digital sequence data. In this talk I will review some of the common problems with the analysis of such data and I will describe a pipeline for the integrated analysis of ChIP-Seq that we have developed in my lab.