Crunch: integrated processing and modeling of ChIP-seq data in terms of regulatory motifs.

ABSTRACT: Although ChIP-seq has become a routine experimental approach for quantitatively characterizing the genome-wide binding of transcription factors (TFs), computational analysis procedures remain far from standardized, making it difficult to compare ChIP-seq results across experiments. In addition, although genome-wide binding patterns must ultimately be determined by local constellations of DNA-binding sites, current analysis is typically limited to identifying enriched motifs in ChIP-seq peaks. Here we present Crunch, a completely automated computational method that performs all ChIP-seq analysis from quality control through read mapping and peak detecting and that integrates comprehensive modeling of the ChIP signal in terms of known and novel binding motifs, quantifying the contribution of

SUBMITTER: Berger S 

PROVIDER: S-EPMC6633267 | biostudies-literature | 2019 Jul

REPOSITORIES: biostudies-literature