Altrans Wiki

Quantification of Splicing Events

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LICENSE

Altrans - Relative quantification of splicing events
Copyright (C) 2012 Halit Ongen, Emmanouil T. Dermitzakis

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/.

INSTALLATION

Windows

You can use the binary at http://sourceforge.net/projects/altrans/files which has been compiled under Cygwin. In order compile it yourself download the latest Cygwin at http://www.cygwin.com/ and follow the instructions provided for Linux and Mac OS. Note that after you have compiled the source under Cygwin in order to run it as a native windows executable you need to have the relevant Cygwin dll’s (for Cygwin 1.7.16-1: cyggcc_s-1.dll, cygstdc++-6.dll, cygwin1.dll, cygz.dll) in your PATH or in the same directory as the altrans binary.

Linux and Mac OS

Tested with GCC version 4.2 or greater.

To install/uninstall follow the steps below:

#Unzip and untar:
    tar -xzvf altrans.vX.X.XX.tar.gz
#Compile:
    cd altrans
    make
#To clean:
    make clean

This should compile, with warnings that can ignored, and create the altrans binary under the bin/ directory. Precompiled binary distributions will also be available at http://sourceforge.net/projects/altrans/files for certain flavours of these OSs, however there is no guarantee that these will run everywhere.

Mac binary was tested and runs on Mac OS X 10.6 & 10.7.
Both linux binaries were tested and run on Ubuntu 8.04 & 10.04 & 12.04, Fedora 14 & 17, SuSE 9.3, and CentOS 5.8.
The linux binary should run on any modern Linux distribution that has the standard C & C++ and zlib libraries.

WORKED EXAMPLE

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Assumes a unix like environment with gcc 4.2 or later.

get the latest altrans and extract

wget http://sourceforge.net/projects/altrans/files/altrans.v1.1.02/altrans.v1.1.02.tar.gz
tar zxvf altrans.v1.1.02.tar.gz

compile

cd altrans
make

get the sample dataset and extract

wget http://sourceforge.net/projects/altrans/files/sampleDataset.tar.gz
tar zxvf sampleDataset.tar.gz
cd sampleDataset

run altrans for both BAM files

../bin/altrans --bam-file Sample1Tissue1_chr22_sorted.bam --annotation gencode.v10.annotation.gtf.chr22.sorted --read-length 75 --output-prefix Sample1Tissue1_chr22 --mapping-quality 150 --check-proper-pairing --split-reads

../bin/altrans --bam-file Sample1Tissue2_chr22_sorted.bam --annotation gencode.v10.annotation.gtf.chr22.sorted --read-length 75 --output-prefix Sample1Tissue2_chr22 --mapping-quality 150 --check-proper-pairing --split-reads

merge the forward and reverse files

../bin/altrans --merge-files .forward --regex "(.+)_.+" --output-prefix allSamples.forward
../bin/altrans --merge-files .reverse --regex "(.+)_.+" --output-prefix allSamples.reverse
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USAGE

Please read the manual.pdf that comes with the software. You can also always try:
altrans -h

Project Admins:

Halit Ongen