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 git@github.com:HarteminkLab/NucID.git
then
cd NucID && python setup.py install
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: