peaKO

Motif elucidation in ChIP-seq datasets with a knockout control | PeaKO discovers motifs in ChIP-seq datasets with knockout controls. PeaKO takes in paired wild-type/knockout BAM files in addition to several reference files, as input. It returns a file of ranked motifs (see our paper for more details) | PeaKO finding transcription factor binding motifs using knockout controls | Denisko D, Viner C, Hoffman MM. Motif elucidation in ChIP-seq datasets with a knockout control. BioRxiv 10.1101/721720 [Preprint]. 2019. Available from: https://doi.org/10.1101/721720 | PeaKO identifies motifs relevant to ChIP-seq experiments by combining two differential analysis approaches. It often improves elucidation of the target motif over other methods and highlights the benefits of knockout controls