https://github.com/esterpantaleo/altra

altra - A Bayesian method for simultaneous transcript reconstruction and abundance estimation with RNA-Seq data from multiple samples.
https://github.com/esterpantaleo/altra

Last synced: 4 days ago
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altra - A Bayesian method for simultaneous transcript reconstruction and abundance estimation with RNA-Seq data from multiple samples.

• Host: GitHub
• URL: https://github.com/esterpantaleo/altra
• Owner: esterpantaleo
• License: gpl-3.0
• Created: 2013-07-31T21:56:56.000Z (over 11 years ago)
• Default Branch: master
• Last Pushed: 2019-10-24T05:20:08.000Z (over 5 years ago)
• Last Synced: 2025-02-11T04:12:45.733Z (4 days ago)
• Language: C++
• Homepage:
• Size: 7.99 MB
• Stars: 0
• Watchers: 2
• Forks: 0
• Open Issues: 0
• Metadata Files:
  • Readme: README.md
  • License: COPYING

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README

        
###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*](https://github.com/arq5x/bedtools2) and [*samtools*](http://samtools.sourceforge.net/) are in your `PATH` and that the [*gsl*](http://www.gnu.org/software/gsl/) and [*boost dynamic_bitset*](http://www.boost.org/doc/libs/1_36_0/libs/dynamic_bitset/dynamic_bitset.html) are installed on your system. Also the software uses *R* and the R package [*FLLat*](http://cran.r-project.org/web/packages/FLLat/index.html).

####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