PT  - JOURNAL ARTICLE
AU  - Danielle Denisko
AU  - Coby Viner
AU  - Michael M. Hoffman
TI  - Motif elucidation in ChIP-seq datasets with a knockout control
AID  - 10.1101/721720
DP  - 2019 Jan 01
TA  - bioRxiv
PG  - 721720
4099  - http://biorxiv.org/content/early/2019/08/28/721720.short
4100  - http://biorxiv.org/content/early/2019/08/28/721720.full
AB  - Chromatin immunoprecipitation-sequencing (ChIP-seq) is widely used to find transcription factor binding sites, but suffers from various sources of noise. Knocking out the target factor mitigates noise by acting as a negative control. Paired wild-type and knockout experiments can generate improved motifs but require optimal differential analysis. We introduce peaKO—a method to automatically optimize motif analyses with knockout controls, which we compare to two other methods. PeaKO often improves elucidation of the target factor and highlights the benefits of knockout controls. It is freely available at https://peako.hoffmanlab.org.