/NucID

A Python package for identifying nucleosomes using single-end DNase-seq data

Primary LanguageJupyter Notebook

NucID: Nucleosome Identification using DNase-seq

NucID is a Python package for identifying nucleosome positions from single-end DNase-seq data:

  • Using DNase-seq data, a Bayes-factor-based nucleosome score can be calculated for any 147 base pair genomic window.
  • Genome-wide nucleosome scores are then determined by applying a simple moving window approach.
  • Finally, a greedy algorithm maps nucleosomes using these genome-wide nucleosome scores.

Install

Clone this repository

git clone git@github.com:HarteminkLab/NucID.git

then

cd NucID && python setup.py install

Dependencies

NucID depends on the following Python packages:

  • Numpy
  • Scipy
  • Pandas

Usage

example.ipynb contains an example on how to calculate moving window nucleosome scores. Each file in the package has an accompany IPython notebook that explains the code.

Pre-computed genome-wide nucleosome scores

We provide pre-computed genome-wide nucleosome scores for both S. cerevisiae genome (sacCer2) and human genome (hg18), available at:

Both were computed using the code here.

Reference

NucID was developed by Jianling Zhong in the Hartemink Lab for the following publication:

Zhong, J., Luo, K., Winter, P. S., Crawford, G. E., Iversen E. S., & Hartemink, A. J. (2016). Mapping nucleosome positions using DNase-seq. Genome Res. gr.195602.115