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Introduction

Dependencies

  • bowtie2
  • primer3
  • python >=3.6:
    • primer3-py
    • biopython
    • beautifulsoup4
    • pysam
    • zipfile36

installation

Checkout repository

#Grab repo from github
git clone https://github.com/gofflab/HCRProbeDesign.git

bowtie2 Installation

To determine whether designed probesets target unique sequences within a given species, we use Bowtie2 to quickly map all designed probesets against a reference genome index (mouse mm10 by default). Please ensure that bowtie2 is installed on your system to use this feature. We recommend using conda to create a specific virtual environment and provide an environment.yml file to install bowtie2 and all other required dependencies for the probe design software.

cd HCRProbeDesign/
conda env create -f environment.yaml
conda activate HCRProbeDesign

pip install

cd ..
pip install ./HCRProbeDesign

Quickstart

Install mm10 bowtie2 index

Before using designProbes, you must either disable genome masking --no-genomemask or install a bowtie2 index into the indices directory <package_dir>/indices/. For mouse (the default target species), we provide a simple command line utility fetchIndex to download and install the mouse mm10 bowtie2 directory into the package reference index folder.

# Grab mm10 index and install in <package_install_dir>/indices/mm10/
$ fetchIndex

Command Line

HCRProbeDesign package provides the commandline executable designProbes as the primary application