Bowtie (not bowtie 2) is recommended to map sequenced short reads either from nucleosome MNase-Seq or histone modification ChIP-Seq. During aligning, -m 1 was recommend to filter multiple mapped tags.

All peaks data from other programs will be indexed by the indexPeak module in NUCLIZE. For successful import, the chromosome, start position and end position information are required for each peak. So that any file formats with these three types information are supported. And the most common file format is bed file.

All called nucleosome peaks (nucleosomePeaks.bed), histone modification peaks (histonePeaks.bed) and differential histone modification peaks between samples (*.diffPeaks.bed) from NUCLIZE could be visualized with IGV or UCSC Genome Browser.

DANPOS, iNPS, and NPS could be employed to call nucleosome peaks.