Software and analysis

Our research combines wet-lab research with bioinformatic analysis.  All code is open-source and is freely available from github.

Featured software

damidseq_pipeline

The damidseq_pipeline software provides automatic alignment, read-extension, normalisation and background reduction for DamID-seq datasets.

polii.gene.call

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

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).

Miscellaneous code

For more information and downloads, please visit Owen’s github site.