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Automated Stripe Identification from contact matrix.

Project description

StripeCaller

A Python implementation of the architectural stripe detecting algorithm described by Vian L et al [1].

Currently, this package contains 3 scripts: call-stripes, pileup-stripes and stripe-plot:

  • call-stripes

    Call stripes from contact matrix. The only required input is the cool URI at certain resolution. The algorithm will detect horizontal (3’) and vertical (5’) stripes separately by searching for consecutive pixels with contact signals significantly higher than the local backgrounds. The output is a single file in bedpe format.

  • pileup-stripes

    This script performs a pileup analysis on stripes.

  • stripe-plot

    Visualize stripes on heatmap.

Installation

stripecaller is developed and tested on UNIX-like operating system, and following packages or softwares are required, which can be installed through conda <Miniconda installer

  1. Python 3.5+
  2. Multiprocess
  3. Numpy
  4. Scipy
  5. Matplotlib
  6. Cooler

First, add some additional channels:

$ conda config --add channels defaults
$ conda config --add channels bioconda
$ conda config --add channels conda-forge

Then execute the following command:

$ conda install multiprocess numpy scipy matplotlib cooler

Finally, install the stripecaller by pip:

$ pip install stripecaller

Usage

Open a terminal, type stripecaller -h for help information.

Citation

[1]Vian, L. et al. The Energetics and Physiological Impact of Cohesin Extrusion. Cell 175, 292-294, doi:10.1016/j.cell.2018.09.002 (2018).

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