###altra

This repository contains altra, a software implementing a Bayesian method for simultaneous transcript reconstruction and abundance estimation with RNA-Seq data in multiple samples. It also contains sim_sam, a software to simulate RNA-Seq data in bam format.

altra is free software, you can redistribute it and/or modify it under the terms of the GNU General Public License.

The GNU General Public License does not permit this software to be redistributed in proprietary programs.

This library 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 . ####Dependences

Installation instructions below assume that the bedtools and samtools are in your PATH and that the gsl and boost dynamic_bitset are installed on your system. Also the software uses R and the R package FLLat.

####Installation

To install the software, clone the repository in ~/src/altra, then:

cd ~/src/altra
make all
make check

and put folder ~/src/altra/scripts in your PATH by adding the following lines to your ~/.bashrc file:

export PATH=$PATH":$HOME/src/altra/scripts/"

After adding this line to your .bashrc, remember to either login again, or do

source ~/.bashrc

####Usage

To print the usage run altra with option -h:

altra -h

or run sim_sam with option -h:

sim_sam -h