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README

README details the structure of the GuideScan development repository

Cloning

When cloning this directory to your machine and running the GuideScan software, please do so in locations with filepaths that do not contain spaces:

Correct Use: /Users/pereza1/Desktop

Incorrect Use: /Users/pereza1/Google\ Drive/

Install

guidescan-crispr

guidescan-crispr contains the package scripts for GuideScan. One directory down contains the installation script for the package

python setup.py build
python setup.py install

This directory also contains a subdirectory entitled trie which contains the C++ code for the trie data structure that GuideScan utilizes. Finally, this directory has a subdirectory entitled guidescan which contains the core scripts upon which the GuideScan package depends.

Dependencies

GuideScan has the following dependencies:

Python Version

  • python 2.7

Non-Python Dependencies

  • samtools version 1.3.1
  • coreutils: specifically shuf
  • rename
  • easy_install

for OSX users these dependencies can be installed via: brew install samtools,brew install rename

for .deb linux users these dependencies can be installed via: sudo apt-get install samtools rename

for .rpm based linux users these dependencies can be installed via: sudo yum install samtools rename

samtools can also be found here: http://www.htslib.org/download/. Unfortunately, versions of samtools <=1.2 are not compatible with GuideScan software.

Python Dependencies

If you run setup.py these installations will be done for you biopython>=1.66 pysam==0.8.3 pyfaidx==0.4.7.1 bx-python==0.7.3

If you desire to compute Rule Set 2 on-target cutting efficiency scores install sklearn==0.16.1 (must be installed by user, https://pypi.python.org/pypi/scikit-learn/0.16.1)