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             Meta analysis of genomic features                                        

  locStack - Meta analysis of genomic features

  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.

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

  Installation Instruction:

  *Prerequisite

  Perl should be installed on your system to run this sortware. It was tested
  perl v5.14.2 but other version should also run it. 

  Before you start, make sure that the following perl modules are available on 
  your system.

  1. CWD
  2. File::Basename
  3. Getopt::Long
  4. Parallel::ForkManager

  The first three modules are part of the standard perl distribution so you are 
  likly to have them if you have perl on your system.

  You can get Parallel::ForkManager module from CPAN at the following link,

  http://search.cpan.org/~yanick/Parallel-ForkManager-1.18/lib/Parallel/ForkManager.pm

  * Installation

  To install locStack, just untar the package at your favorite place.

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

  perl <full path to parent directory>/locStack/bin/locStack.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 locStack="<full path to parent directory>/locStack/bin/locStack.pl"

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

  User Manual:

  Usage: : locStack.pl < -exp ALIGNEDREADS -summit REFERENCECOORDS -o NAME -g GENOME > [Options]

  Options:

  -h, --help              Show the help message and exit

  -a, --aln               Bed file of aligned reads (REQUIRED)
                          The bed file may contain the scores/weights in a 
                          column. In that case the scores/weights may be 
                          used in calculating distribution in combination 
                          with flag -s,--score option. (see below)

  -r, --ref               Bed file of reference coordinates. 
                          The start position of the interval is considered
                          as zero (starting point) while calculating 
                          distribution.

  -u, --up                Window downstream of the reference coordinates
                          This is the "right" bound of the distribution. 
                          (Default 1000)

  -d, --down              Window downstream of the reference coordinates             
                          This is the "left" bound of the distribution.
                          (Default 1000)

  -b, --bin               Size of each bin in bp
                          (Default 100)

  -c, --control           Bed file of control reads (optional)
                          This option is only useful if -a,--aln is used
                          with -s,--score option. When this option is 
                          used the scores in this file are subtracted 
                          from the scores at the corresponding positions
                          in the file given with -a,--aln option 

  -t, --thread            Number of processors to be used 
                          (Default 2)

  -s, --score             If the scores/weights in the file given with -a,
                          --aln file are to be used. y=yes; n=no 
                          (Default n)

 -f, --field              Column/field in the bed file that contains the 
                          scores/weights. With option is only valid is -s,
                          --score option is used.
                          (Default 5)

 -n, --normalize          Total number of reads aligning in a segment will 
                          be normalized with this number using the formula
                          NR = A * N / T
                          Where:
                             NR= Normalized Reads
                              A= Aligned Reads
                              N= No given with -n option
                              T= Total number of reads in --aln file
                          (Default no normalization)


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