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.
Clone this repository
git clone [email protected]:HarteminkLab/NucID.git
then
cd NucID && python setup.py install
NucID
depends on the following Python packages:
- Numpy
- Scipy
- Pandas
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.
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.
NucID
was developed by Jianling Zhong in the Hartemink Lab for the following publication: