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---quadraG v0.1---

quadraG

quadraG: a fast multithreading based tool to detect G-quadruplexes in genome or transcriptome sequences

Copyright 2017 Jitendra Narayan jnarayan81@gmail.com ; Rahul Agarwal vibes1002003@gmail.com

quadraG is currently in active development and is not ready for general use. The software will be fully described in a forthcoming publication.

LICENSE

quadraG 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, either version 3 of the License, or (at your option) any later version.

quadraG is distributed with the hope that it will be useful for reseachers worldwide, 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 quadraG, in a file called COPYING. If not, see http://www.gnu.org/licenses/.

INSTALLATION

See INSTALLATION steps below:

1. Edit setup.sh and change $PATH to the full directory where you've placed the package.

2. To automatically place the package into your environment, add

   source /setup.sh to your .bash_profile

Be sure to source your .bash_profile (or just setup.sh) before using quadraG

USING PERL 5.x

quadraG does not support Perl 5.x, and no plans exist to provide such support. For a strong biological analysis package for perl 5, see perl https://www.perl.org/ and bioperl: http://bioperl.org/

Perl modules

You also need to have Perl, BioPerl, and some other modules installed in your machine:

Bio::SeqIO
Bio::AlignIO
Cwd
File::chdir
File::Copy
POSIX
Statistics::Distributions
Statistics::Multtest
Tie::File
Try::Tiny
Data::Dumper
File::Spec::Functions
File::Basename
FindBin
Capture::Tiny
Getopt::Long

You can check if above mentioned modules installed in your machine with 'perl -M -e 1'. It will return an error message if it isn't installed.

E.g. "perl -MBio::SeqIO -e 1"

To install these modules, you can do either through the CPAN or manually downloading (http://search.cpan.org/) and compiling them. To use CPAN, you can do by writing:

perl -MCPAN -e 'install '

To install manually, search for the most recent version of these modules and, for each, download and type the following (should work most of the time, except for modules like BioPerl, of course):

tar -zxvf <module.tar.gz> perl Makefile.PL make make test make install

For more detail, you could visit: http://bioinformaticsonline.com/blog/view/710/how-to-install-perl-modules-manually-using-cpan-command-and-other-quick-ways

DOCUMENTATION

For documentation, see quadrqG_manual.pdf in the base project folder.

This documentation may be out of date depending on whether or not the developers did their job and re-generated the documentation before the release. If you suspect that the documentation is out of date, or if you are using code from the repository (and not from a release), you can re-generate the documentation or contact the authors.

RELEASE HISTORY

0.1.O - 30 Jun 2017

OUTPUT FORMAT

quadraG outfile columns:

* CHROM       Reference entry where quadraG occurs
* OUTERSTART  The 5' most boundary estimate of where quadraG begins
* START       Best guess as the the exact start of the quadraG
* INNERSTART  The 3' most boundary estimate of where quadraG begins
* INNEREND    The 5' most boundary estimate of where quadraG ends
* End         Best guess as the the exact end of the quadraG
* OUTEREND    The 3' most boundary estimate of where the quadraG ends
* TYPE        Variant type. One of MIS, INS, INSZ, or DEL
* SIZE        Estimate size of the quadraG
* INFO        More information associated with the calls

quadraG result columns:

* ID        Unique identifier of the call
* CHROM     Reference entry where q4 occurs
* START     Start point
* END       End point
* EXSEQ     Average amount of sequence left between
* GFF       GFF entry

quadraG tabfile column

* SEQ       quadraG seauence
* NAME      Name of the quadraG
* REFNAME   Reference name
* START     Start coordinate of quadraG
* END       End coordinate of quadraG
* MUTATION  Number of random mutation
* SIZE      Size of the quadraG
* STRAND    Strand of of the quadraG
* ISLAND    Number of G island
* SCORE     Score of the quadraG

ANNOTATION DESCRIPTIONS

Coming Soon

EXTRA

Coming Soon

FAQ

Can I report bugs or ask questions? Please report your issues to ticketing system.

CONTRIBUTION

Feel free to clone this repository and use it under the licensing terms.

Additionally, as the project is on github, you may submit patches, ticket requests, edit the wiki, send pull requests - anything you like and have the permissions to do. I will encourage any suggestions from followers :)

As always, you can contact the authors at jnarayan81@gmail.com or vibes1002003@gmail.com.