Practical Guidelines for the Comprehensive Analysis of ChIP-seq Data

• DOI: 10.1371/journal.pcbi.1003326
• Publication Date: 2013-11-14T22:30:48Z
• Authors: Timothy Bailey; Pawel Krajewski; Istvan Ladunga; Celine Lefebvre; Qunhua Li; Tao Liu; Pedro Madrigal; Cenny Taslim; Jie Zhang
• Keywords: ENCODE; ChIP-sequencing; Chromatin immunoprecipitation

Mapping the chromosomal locations of transcription factors, nucleosomes, histone modifications, chromatin remodeling enzymes, chaperones, and polymerases is one key tasks modern biology, as evidenced by Encyclopedia DNA Elements (ENCODE) Project. To this end, immunoprecipitation followed high-throughput sequencing (ChIP-seq) standard methodology. such protein-DNA interactions in vivo using ChIP-seq presents multiple challenges not only sample preparation but also for computational analysis. Here, we present step-by-step guidelines analysis data. We address all major steps data: depth selection, quality checking, mapping, data normalization, assessment reproducibility, peak calling, differential binding analysis, controlling false discovery rate, annotation, visualization, motif At each step our discuss some software tools most frequently used. highlight problems associated with a concise workflow Figure 1 that complements expands on recommendations ENCODE modENCODE projects. Each described detail following sections.