De novo detection of differentially bound regions for ChIP-seq data using peaks and windows: controlling error rates correctly.

ABSTRACT: A common aim in ChIP-seq experiments is to identify changes in protein binding patterns between conditions, i.e. differential binding. A number of peak- and window-based strategies have been developed to detect differential binding when the regions of interest are not known in advance. However, careful consideration of error control is needed when applying these methods. Peak-based approaches use the same data set to define peaks and to detect differential binding. Done improperly, this can result in loss of type I error control. For window-based methods, controlling the false discovery rate over all detected windows does not guarantee control across all detected regions. Misinterpreting the former as the latter can result in unexpected liberalness. Here, several solutions are presented to

SUBMITTER: Lun AT 

PROVIDER: S-EPMC4066778 | biostudies-literature | 2014 Jun

REPOSITORIES: biostudies-literature