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

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:

• sacCer2
• hg18

Both were computed using the code here.