DeNovo ChIP-Seq Analysis

Chromatin immunprecipitation sequencing (ChIP-Seq) is routinely used to study the binding preferences of transcription factors (TFs) and to determine epigenetic regulation. Several methods have been developed to analyze ChIP-Seq data to determine the DNA binding motifs of the TFs being studied. These methods start by aligning the short reads to a reference genome to identify peaks; locations in the genome, which are enriched in the case experiment when compared to a control. While such alignment-based methods are often successful, they are not appropriate for cases where a reference genome is not available or when the analyzed genome is different from the reference genome (e.g., in cancer). Here we develop and apply methods for de novo analysis of ChIP-Seq data that do not rely on a reference genome. We start by de novo assembly of the short reads grouping them to identify longer contigs (termed chiptigs).

Results for the Cancer Analyses in the Paper