Chromatin accessibility: a window into the genome

Table 2 Chromatin accessibility high-throughput sequence data analysis

	Detection of enriched regions	Estimation of nucleosome organization and TF occupancy metrics
MNase-seq	1. GeneTrack [126]	1. Nucleosome positioning algorithms [48, 58, 111, 144]
	2. Template filtering algorithm [58]	2. Nucleosome occupancy algorithms [48, 145]
	3. DANPOS [109]	3. V-plots for TF occupancy [50]
	4. iNPS [127]	3. V-plots for TF occupancy [50]
DNase-seq	1. F-Seq [129]	1. Digital genomic footprinting algorithms [19, 78, 83, 85, 128, 146–149].
	2. Hotspot, DNase2Hotspots [21, 130]	2. Nucleosome and TF occupancy algorithms [150]
	3. ZINBA [131]	3. CENTIPEDE [151]
	4. MACS [132]	3. CENTIPEDE [151]
FAIRE-seq	1. MACS2; https://github.com/taoliu/MACS/, [132]	Not available
FAIRE-seq	2. ZINBA [131]	Not available
ATAC-seq	1. ZINBA [131]	1. Digital genomic footprinting algorithms [19, 78, 83, 85, 128, 146, 149]
ATAC-seq	2. MACS2; https://github.com/taoliu/MACS/, [132]	2. CENTIPEDE [151]
	3. Hotspot, DNase2Hotspots [21, 130]

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