Nucleosome positioning utilities

Software utility for QC and evaluation of nucleosome positioning data from MNase-Seq or DNase-Seq experiments.

Input data

• BAM/SAM mapping of MNase-Seq reads to reference genome. Original sequencing data must have been paired-end sequencing.
• Fasta file of reference genome sequence
• GFF file of genomic features corresponding to sequence file

Output data

• DNA fragment length histogram, evaluates effectiveness of digestion
• Nucleosome occupancy map (simply coverage pileup for specific fragment range)
• Nucleosome absolute positioning map (using nucleosome centers rather than read starts)
  • With the high-accuracy procedure of Cole (2012)
  • With broader fragment range
  • Smoothed positioning map
  • Occupancy map (smoothing with uniform kernel and width 73)
• Nucleosome conditional positioning map (like Kaplan 2010)
• Nucleosome global phaseogram (using nucleosome centers vs read starts)
• Nucleosome localization measure map (using procedure of Zhang et al.)
• Nucleosome calls (using iterative procedure of Kaplan et al 2010)
• Nucleosome feature-specific phaseogram (e.g. relative to TSS)
• Well positioned nucleosome array calls (using FFT procedure)