Protein Occupancy Profiling Pipeline

The Protein Occupancy Profiling Pipeline streamlines the analysis of protein occupancy profiling data and compares different experiments across conditions. To this end, we have implemented a number of modules that perform the following analysis steps: read processing, read mapping, transcriptome-wide read coverage and position-specific T-C transition event profiling as well as global comparison to genomic features and across different experiments (e.g. calling differentially occupied sites). All analysis steps produce diagnostic plots as well as text statistics combined in an HTML file that can directly be used for quality assessment of profiling experiments.