NucleoDetective

Differential nucleosome positioning analysis unravels differences in nucleosome array configurations between biological conditions. Nucleosome positions can be determined based on fragmentation patterns created during the ATAC-seq assay. By evaluating fragment length distribution at each position and comparing it to a background, NucleoDetective (NDetect) is able to calculate a nucleosomal signal across peak regions in the genome and predict nucleosome positions based on it.
Furthermore, other metrics describing the predicted nucleosomes individually and in relation to one another are derived from the prediction. Afterwards, individual conditions are compared to each other and peaks with differential nucleosome patterns are identified. Peak intersecting Transcription Start Sites (TSS) are assessed in a separate downstream analysis.