Sensitive and robust assessment of ChIP-seq read distribution using a strand-shift profile | Zendy

Ryuichiro Nakato | Zendy; Katsuhiko Shirahige | Zendy

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Sensitive and robust assessment of ChIP-seq read distribution using a strand-shift profile

Author(s) -

Ryuichiro Nakato,

Katsuhiko Shirahige

Publication year - 2018

Publication title -

bioinformatics

Language(s) - English

Resource type - Journals

SCImago Journal Rank - 3.599

H-Index - 390

eISSN - 1367-4811

pISSN - 1367-4803

DOI - 10.1093/bioinformatics/bty137

Subject(s) - computer science , false positive paradox , software , data mining , source code , chromatin immunoprecipitation , chip , metric (unit) , pattern recognition (psychology) , artificial intelligence , biology , genetics , telecommunications , gene expression , promoter , gene , programming language , operating system , operations management , economics

Chromatin immunoprecipitation followed by sequencing (ChIP-seq) can detect read-enriched DNA loci for point-source (e.g. transcription factor binding) and broad-source factors (e.g. various histone modifications). Although numerous quality metrics for ChIP-seq data have been developed, the 'peaks' thus obtained are still difficult to assess with respect to signal-to-noise ratio (S/N) and the percentage of false positives.

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