Shape-based peak identification for ChIP-Seq

Table 4 Parameters used in T-PIC

Parameters used in T-PIC.
Parameter	Brief Description	Value used in testing
L	average fragment length	N/A(varies by experiment)
	minimum length of peak (in bp)	10
α	significance p-value	0.01
	width of interval used to calculate local rate γ(t)	1,000
K	minimum length of interval for discretizing γ	10,000 (human)
		5,000 (D. Melano.)
D	used in discretizing γ	5
C	using in selecting height h	7
	number of random trees per region in simulation	30,000

The parameters involved in the T-PIC algorithm are presented as well as the values used in the Testing section. Further details on each parameter may be found in the Algorithm section.