Pipeline to improve transcript annotation based on RNA-seq and ChIP-seq data.
The current version has been used to annotate the Xenopus laevis genome based on experimental data.
However, it is not yet easy to install and use as the documentation is incomplete. In addition the tools have not been thoroughly tested on a clean installation, which means I'm not sure all dependencies have been correctly specified.
The following Python modules are required:
- GFF parser - http://github.com/chapmanb/bcbb/tree/master/gff
- Biopython - http://biopython.org/
- pysam ( >= 0.9)
- pyyaml
- networkx (== 1.9)
- GimmeMotifs - http://github.com/simonvh/gimmemotifs
- HTSeq - http://www-huber.embl.de/users/anders/HTSeq/doc/overview.html
- numpy
# install prerequisites
git clone git@github.com/simonvh/pita.git
cd pita
python setup.py test
sudo python setup.py install