Table 1.
Comparison of four tools for pile-up analysis across a set of features: Juicer Aggregate Peak Analysis (APA) (Rao et al., 2014), HiCExplorer (hicAggregateContacts and hicAverageRegions) (Ramírez et al., 2018) and GENOVA (APA, ATA and PE-SCAn) (van der Weide, 2019) and coolpup.py
| Feature | Juicer | HiCExplorer | GENOVA | coolpup.py |
|---|---|---|---|---|
| Aggregate loops | + | − | + | + |
| Aggregate region pairs | − | + | + | + |
| Interactions between two region sets | − | + | − | + |
| Local pile-ups | − | + | − | + |
| (Local) rescaled pile-ups | − | − | + | + |
| Distance normalization | − | Expected (and z-score) | Fixed shifts (for pairwise analysis) | Expected or random shifts |
| Coverage normalization | − | − | − | + |
| Anchored pile-ups/loop-ability | − | − | − | + |
| Command-line interface | + | + | − | + |
| Simple text output of pile-ups | + | + | − | + |
| Hi-C file format | .hic | .cool, .h5, other? | HiC-pro | .cool |