Bio-ViennaNGS-SpliceJunc
========================

Bio::ViennaNGS::SpliceJunc is a Perl module for Alternative Splicing (AS)
analysis. It provides routines for identification and characterization of
novel and existing (annotated) splice junctions from RNA-seq data.

Identification of novel splice junctions is based on insecting potentially
novel splice junctions from RNA-seq data with annotated splice junctions.

INSTALLATION

To install this module type the following:

   perl Makefile.PL
   make
   make test
   make install

DEPENDENCIES

This module requires these other modules and libraries:

   Bio::ViennaNGS >= 0.09
   IPC::Cmd
   Path::Class
   Carp

Bio::ViennaNGS::SpliceJunc uses third-party tools for computing
intersections of BED files: *bedtools intersect* from the BEDtools
<http://bedtools.readthedocs.org/en/latest/content/tools/intersect.html>
suite is used to compute overlaps and *bedtools sort* is used to sort BED
output files. Make sure that those third-party utilities are available on
your system, and that hey can be found and executed by the perl
interpreter. We recommend installing the latest version of BEDtools
<https://github.com/arq5x/bedtools2> on your system.

AUTHOR

Michael T. Wolfinger <michael@wolfinger.eu>

COPYRIGHT AND LICENCE

Copyright (C) 2014 Michael T. Wolfinger <michael@wolfinger.eu>

This library is free software; you can redistribute it and/or modify
it under the same terms as Perl itself, either Perl version 5.16.3 or,
at your option, any later version of Perl 5 you may have available.

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.
