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README
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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 narekum@gmail.com or narendra.kumar@glasgow.ac.uk
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)
===============================================================================
** END OF THE FILE **