Pipeline to improve transcript annotation based on RNA-seq and ChIP-seq data.

It has been used to annotate the Xenopus laevis genome based on experimental data.

Session et al. Genome evolution in the allotetraploid frog Xenopus laevis. Nature. 2016 Oct 20;538(7625):336-343. doi: 10.1038/nature19840.

However, it is not yet easy to use as the documentation is incomplete.

Pita can combine imprecise and/or incomplete gene models with experimental data such as RNA-seq and H3K4me3 ChIP-seq to create improved gene annotation. Features:

• Graph-based annotation capable of incorporating diverse types of data
• Improved annotation of 5' end of genes by prioritizing promoters with H3K4me3
• UTR annotation based on RNA-seq data in combination with change-point detection

Clone this repository:

$ git clone git@github.com/simonvh/pita.git
$ cd pita

Install dependencies via conda:

$ conda env create -f environment.yml

Activate the environment:

$ source activate pita

Test & install:

$ python setup.py test
$ python setup.py install