########################
# version1.4
# modification 2012/06/09
##########################
<one line to give the program's name and a brief idea of what it does.>
Copyright (C) <2011> <Yang Li (yangli9@illinois.edu)>
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, either version 3 of the License, or
(at your option) any later version.
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/>.
############################
To install FusionHunter
type:
./install.sh
FusionHunter utilize perl package ForkManager. install.sh shall help you install ForkManager Package.
To install ForkManager package, you should have sudo permission
####################
FusionHunter use Bowtie as alignment tool. The bowtie and bowtie-build (all for 64-bit) are in path of FusionHunter/bin,
if your mathine type is 32-bit, you can copy the executable file 'bowtie', 'bowtie-build' in FusionHunter/src/bowtie-0.12.7-linux-i386/
into FusionHunter/bin (replace the original ones for 64-bit)
####################
To run FusionHunter
copy the file FusionHunter.cfg to your working dir and edit variables in FusionHunter.cfg as indicated
then type following in your working dir:
DirtoFusionHunter/bin/FusionHunter.pl FusionHunter.cfg
For more information, please see http://bioen-compbio.bioen.illinois.edu/FusionHunter/
#######################
Please cite:
Li Y, Chien J, Smith DI, and Ma J. FusionHunter: identifying fusion transcripts in cancer using paired-end RNA-seq. Bioinformatics, 27(12):1708-10, 2011.