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This subdirectory contains the example scripts to accompany the manuscript.  Read the section [Version your code][version] for the full explanation.  The commands described below should be executed from within the subdirectory `code`.  [version]: https://www.authorea.com/users/5990/articles/17489/_show_article#article-paragraph-version__minus__your__minus__code__dot__tex-landing-welcome  ## process.sh  `process.sh` downloads the ENCODE CTCF ChIP-seq data from multiple types of kidney samples and calls peaks.  The downloaded BAM files and [MACS2][] output are saved in tissue-specific subdirectories in `../data/`.  Run it as follows:  ```bash  bash process.sh  ```  You will need to have Python 2.7 installed because it is a [prerequisite][] for the peak caller [MACS2][].  To install MACS2, run:  ```bash  pip install macs2  ```  [prerequisite]: https://github.com/taoliu/MACS/blob/master/INSTALL.rst#prerequisites  [MACS2]: https://github.com/taoliu/MACS  ## clean.py  `clean.py` filters peaks with a fold change cutoff and merges peaks from the different kidney samples.  It creates the file `../data/sites-union.bed`.  Run it as follows:  ```bash  python clean.py  ```  It can be run with either Python2 or Python3.  You will first need to install [bedtools][] and [pybedtools][].  See their documentation for instructions, but as an example, this can be accomplished on Ubuntu with the following:  ```bash  apt-get install bedtools  pip install pybedtools  ```  [bedtools]: http://bedtools.readthedocs.org/en/latest/content/installation.html  [pybedtools]: http://pythonhosted.org/pybedtools/main.html  ## analyze.R  `analyze.R` creates diagnostic plots on the length of the peaks and their distribution across the genome.  It creates the file `../data/sites-union.pdf`.  Run it as follows:  ```bash