A package for the processing of NucleaSeq data, as described in the manuscript:
Stephen K. Jones Jr, John A. Hawkins, Nicole V. Johnson, Cheulhee Jung, Kuang Hu, James R. Rybarski, Janice S. Chen, Jennifer A. Doudna, William H. Press, and Ilya J. Finkelstein
bioRxiv
The following instructions should work across platforms, except that installing virtualenv with apt-get is Ubuntu specific. For other platforms, install virtualenv appropriately if desired.
First, clone the repository to a local directory:
git clone https://github.com/finkelsteinlab/nucleaseq.git
Optionally, you can install into a virtual environment (recommended):
sudo apt-get install -y virtualenv
cd nucleaseq
virtualenv envnucleaseq
. envnucleaseq/bin/activate
Now install dependencies:
pip install numpy==1.13.3 && pip install cython==0.24 && pip install -r requirements.txt
Note that some versions of pip require each line of the requirements.txt file be installed in a separate call.
Next install the freebarcodes package in the same virtual environment, found at https://github.com/hawkjo/freebarcodes.
Finally, install nucleaseq with
python setup.py install
NucleaSeq data processing and analysis is memory intensive. All work for the original paper was performed on a server with 256GB of RAM. Less is possible with reduced the parallelization, but results in correspondingly slower runtimes. Memory usage also depends on library design, and analysis of the original experiments required at least 64GB of RAM. For the first run, monitor memory use carefully, and select the machine and parallelization accordingly.
The NucleaSeq pipeline is a combination of command line invocations and Jupyter notebooks,
typically performed in the order below. The notebooks are located in the notebooks folder and
contain instructions for their use.
Notebook: NucleaSeq Oligo Design.ipynb
Command line:
nucleaseq setup_run ...
nucleaseq preprocess ...
Type nucleaseq --help for details.
Notebooks, in the following order:
NucleaSeq Full Data Tabulation and Normalization Factors.ipynb
NucleaSeq Full Data Analysis.ipynb
NucleaSeq Cut Data Processing.ipynb
The CRISPR Model described in the paper is available in this software package. Its use is explained
in the notebook CRISPR Model Calculator Tutorial.ipynb.