This is a repository to analyze the live-cell imaging data of cohesin and DNA.
The conda environment to run the pipeline can be found in the environment folder
To install it type:
conda env create -f environment/environment_cohesin_analysis.yml
The workflow is written to be used with snakemake. No installation is required to run the workflow, simply the conda environment.
The steps and code to execute the workflow is contained in the Snakefile document.
A simplified visual representation of the workflow is shown below:
To run the pipeline cd in this folder and type:
snakemake -cores 1
With -cores n, n being the number of cores you want to use. If no core argument is given, the number of used cores is determined as the number of available CPU cores in the machine.
If you want a dry run showing all the steps
snakemake -np
To visualize the DAG (directed acyclic graph) which corresponds to a vizualization of the workflow with the different steps you can write:
snakemake --forceall --dag | dot -Tpdf > dag.pdfThe whole pipeline is written in python, all the function used by snakemake can be found in utils. All the packages necessary for the execution of utils are in the enivironment. In the notebook test_workflow.ipynb you can run all the steps without using snakemake.
In this repository you will find jupyter-notebooks allowing to analyze the results of the pipeline. Mainly: analyze_results.ipynb and visualize_results.ipynb.