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    _____ _     _____ _____                       
   / ____| |   |_   _|  __ \                      
  | |    | |__   | | | |__) |_____ ___  ___  __ _ 
  | |    | ._ \  | | |  ___/______/ __|/ _ \/ _` |
  | |____| | | |_| |_| |          \__ \  __/ (_| |
   \_____|_| |_|_____|_|          |___/\___|\__, |
    Bowtie2, Fastqc, Samtools                  | |
   ____  _            _ _                      |_|
  |  _ \(_)_ __   ___| (_)_ __   ___ 
  | |_) | | '_ \ / _ \ | | '_ \ / _ \
  |  __/| | |_) |  __/ | | | | |  __/
  |_|   |_| .__/ \___|_|_|_| |_|\___|
          |_|                        
  

  Institute of Cancer Sciences
  Epigenetics Unit
  University of Glasgow
  Garscube Estate
  Glasgow G61 1QH

  Report bugs to [email protected] or [email protected]

  Copyright 2016 Narendra Kumar

  This program is free software; you can redistribute it and/or modify 
  it under the terms of the GNU General Public License as published by
  the Free Software Foundation; version 3 of the License.

  This program is distributed in the hope that it will be useful,
  but WITHOUT ANY WARRANTY; without even the implied warranty of 
  MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
  GNU General Public License for more details.

  You should have received a copy of the GNU General Public License
  along with this program; if not, see <http://www.gnu.org/licenses/>
  or write to the Free Software Foundation, Inc., 51 Franklin Street,
  Fifth Floor, Boston, MA 02110-1301, USA.

  Python scripts bedToBedGraph.py and extendbed were written by Tony McBryan.

  ==============================================================================

  *Prerequisite

  Install the following programs on your system

  1. Bowtie2 Fast and sensitive read alignment
     http://bowtie-bio.sourceforge.net/bowtie2/index.shtml

  2. FASTQC
     http://www.bioinformatics.babraham.ac.uk/projects/fastqc/

  3. SAMtools
     http://samtools.sourceforge.net/

  4. bedtools: a powerful toolset for genome arithmetic
     http://bedtools.readthedocs.io/en/latest/index.html

  5. Following programs from UCSCtools
     http://hgdownload.cse.ucsc.edu/admin/exe/linux.x86_64/ (for 64 bit linux)
     fetchChromSizes
     bedGraphToBigWig
     

  *Installation

  1. To install ChIP-seq pipeline, untar the package at your favorite place.

  2. Change the value of variables in lines from 83 to 91 to the appropriate 
     location of the program on your system  

     Make sure you set the path to the index files of the genomes for 
     bowtie2. You may download from the following locations.

     http://bowtie-bio.sourceforge.net/bowtie2/index.shtml
     http://support.illumina.com/sequencing/sequencing_software/igenome.html

  You can now start using by giving the full path of the perl script

  perl <full path to parent directory>/bin/bowtie2Pipeline.pl <options>

  You may make an alias of executable as use it from anywhere without having 
  to write full path

  Add following line in your ~/.bashrc file 

  alias bowtie2Pipeline="<full path to parent directory>/ChIPseq_Pipeline/bin/bowtie2Pipeline.pl"


  *User manual

  Usage: bowtie2Pipeline.pl < --dir MAPDIRECTORY --species SPECIES --quals QUALS > [Options]

  Options:

    -h, --help       Show this help message.

    -d, --dir        directory where sequences are kept  (required)

    -s, --species    species e.g. hg19  (required)

    -q, --quals      quals (required)
                     available quals: phred33-quals
                                      phred64-quals
                                      solexa-quals
                                      solexa1.3-quals
                                      integer-quals
    -t, --threads    number of processors to be used (default 2)

    -e, --extra      extra bowtie options enclosed in quote ""

    -z, --zip        zip the fastq files after the run y=yes; n=no (default y)

    -i, --insertsize extend the reads to this length (default 150)

  Examples:
  $ perl bowtie2Pipeline.pl --dir mapdirectory --species hg19 --quals phred33-quals
  \or\
  $ perl bowtie2Pipeline.pl  -d mapdirectory -s hg19 -q phred33-quals -t 8 -z n -i 150


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