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1.  Processing and analyzing ChIP-seq data: from short reads to regulatory interactions 
Briefings in Functional Genomics  2010;9(5-6):466-476.
Chromatin-immunoprecipitation and sequencing (ChIP-seq) is a rapidly maturing technology that draws on the power of high-throughput short-read sequencing to decipher chromatin states with unprecedented precision and breadth. Although some aspects of the experimental protocol require careful tuning, the bottleneck currently firmly lies with the downstream data analysis. We give an overview of the better-established aspects of genome mapping and data normalization and we describe the more recent progress in peak calling and their statistical analysis and provide a brief overview of popular follow-up analyses such as genomic feature categorization and motif search.
doi:10.1093/bfgp/elq022
PMCID: PMC3080774  PMID: 20861161
ChIP-seq; high-throughput sequencing; DNA binding; transcriptional regulation; bioinformatics

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