The RRBSseeqer package performs analysis of RRBS DNA methylation data.
RRBSseeqer is still under development, but we can make it available to you if you want to try it. Send us an email at firstname.lastname@example.org
A tutorial is available at http://icb.med.cornell.edu/wiki/index.php/Elementolab/RRBSseeqer_Tutorial; however many functionalities are not described in the tutorial.
RRBSseeqer requires a modern C/C++ compiler and works in Linux and MacOS environments.
Elemento lab members and collaborators can get the latest source code from our SVN server:
svn co https://pbtech-vc.med.cornell.edu/public/svn/elementolab/RRBS/trunk RRBSseeqer/ svn co https://pbtech-vc.med.cornell.edu/public/svn/elementolab/BIO-C/trunk BIO-C/ svn co https://pbtech-vc.med.cornell.edu/public/svn/elementolab/PERL_MODULES/trunk PERL_MODULES/
(you can use --username=guest --email@example.com if you don't have a pbtech account)
Also, you need to install the apophenia library.
Compilation and installation
Once you have obtained the code, you will need to type the following commands:
cd RRBSseeqer/ make
cd PERL_MODULES echo export PERLMODUELSDIR=`pwd` >> ~/.bashrc # add environment variable to startup script; note the inverted quotes ! source ~/.bashrc