NucSeq v1.0

Description

NucSeq is a multi-threaded nucleosome sequencing analysis package.

Installation

1. Clone the repository:

   git clone [email protected]:jordiabante/nucleosome_positioning.git 
   

2. Add the bin folder in the repository to your path variable by adding the following line to the .bashrc (.bash_profile in Mac) file:

   export PATH="path/to/bin:$PATH"
   

3. If the machine running the code is Machintosh install coreutils (sudo port install coreutils) as well as: sed, gzip, grep, getopt, mysql, openssl, readline, boost, zlib. Add the following line to the .bashrc (.bash_profile in Mac) file:

   export PATH="/opt/local/bin:$PATH"
   export PATH="/opt/local/libexec/gnubin:$PATH"
   

Dependancies

1. samtools
2. bedtools
3. bowtie2

Usage

1. Every folder (script_name) will contain the following files and directories:
   1. sript_name.sh: bash script
   2. main/
      • main.sh: bash script to try the command with toy example.
      • Files required for the toy example.