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Perm-seq: Mapping Protein-DNA Interactions in Segmental Duplication and Highly Repetitive Regions of Genomes with Prior-Enhanced Read Mapping

Xin Zeng, Bo Li, Rene Welch, Constanza Rojo, Ye Zheng, Colin N. Dewey, Sündüz Keleş, Kevin Chen
2015 PLoS Computational Biology  
We developed Perm-seq, a prior-enhanced read allocation method for ChIP-seq experiments, that can allocate multi-mapping reads in highly repetitive regions of the genomes with high accuracy.  ...  We applied Perm-seq to 64 ENCODE ChIPseq datasets from GM12878 and K562 cells and identified many novel protein-DNA interactions in segmental duplication regions.  ...  Katherine Pollard of Gladstone Institutes, UC San Francisco for discussions on the phyloP scores. We thank the Keleş Research Group for many useful discussions and feedback. Author Contributions  ... 
doi:10.1371/journal.pcbi.1004491 pmid:26484757 pmcid:PMC4618727 fatcat:vwjdrjyi4rdqthcslxdhciu54e