Software and analysis
Our research combines wet-lab research with bioinformatic analysis. All code is open-source and is freely available from github.
The damidseq_pipeline software provides automatic alignment, read-extension, normalisation and background reduction for DamID-seq datasets.
The polii.gene.call script will call genes with significantly enriched RNA pol II occupancy. It is designed for use with Targeted DamID RNA pol II datasets.
find_peaks is a simple yet robust FDR peak caller. It was designed for use with DamID-seq datasets, but can be used on any file in bedgraph format (including ChIP-seq data).
For more information and downloads, please visit Owen’s github site.