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