Comparative study on chromatin loop callers using Hi-C data reveals their effectiveness

BMC Bioinformatics

Table 5 Representation of every tool performance in different categories

Tools	Biological feature (CTCF, H3K27ac, RNAPII)	Consistency	Robustness in parameters	Computational efficiency: running time	Computational efficiency: memory
LASCA	*	**	*	*	**
cLoops***	***	***	**	**	*
cLoops2***	*	***	*	*	**
HiCExplorer**	**	**	***	**	*
FitHiC2	*	***	*	*	***
FitHiChIP	***	**	*	*	***
Peakachu	**	*	**	***	***
Mustache	*	**	***	***	**
Chromosight	***	*	*	***	*
SIP	**	*	**	**	**
HiCCUPS*	**	**	***	**	*

Star (*) symbol tells the performance category of every individual tools. Tools are categorized in terms of performance in three categories: Excellent (***), Good (**), and Fair (*). HiCCUPS* and HiCExplorer** didn’t produce results at low resolutions and cLoops*** and cLoops2*** do not have a resolution parameter

ISSN: 1471-2105