Release version 1.1 of origami, a pipeline for processing, mapping, and analysis of ChIA-PET data sets. This is the initial full release of this software pipeline.
A brief summary of the features of this pipeline are:
- Processing ChIA-PET paired-end tags, and this pipeline can handle paired-end tags with both the AB-linker (Fullwood et al 2009)and bridge-linker (Tang et al 2015) protocols
- Mapping of ChIA-PET paired-end tags to the genome
- Analysis and modeling of mapped paired-end tags to call high-confidence interactions connecting enriched ChIP peaks. This modeling corrects for sequencing depth and distance-related biases in ChIA-PET data and adapts to different data sets to identify the PET count cutoff that statistically separates peak to peak contacts that appear interacting versus non-interacting