ChIP-Seq peak calling and data analysis in woody plants
Chromatin immunoprecipitation (ChIP) followed by highthroughput sequencing (ChIP-Seq) provides an important tool to study genome-wide protein-DNA interactions to help understand gene regulation in the context of native chromatin. A complete ChIP-Seq workflow including peak calling, peak classification, transcription factor binding site overrepresentation and definition of new TFBS motifs. In this paper, ChIP-Seq peak calling and data analysis is described in detail.
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