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Table 2 Chromatin accessibility high-throughput sequence data analysis

From: Chromatin accessibility: a window into the genome

 

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]

DNase-seq

1. F-Seq [129]

1. Digital genomic footprinting algorithms [19, 78, 83, 85, 128, 146149].

2. Hotspot, DNase2Hotspots [21, 130]

2. Nucleosome and TF occupancy algorithms [150]

3. ZINBA [131]

3. CENTIPEDE [151]

4. MACS [132]

FAIRE-seq

1. MACS2; https://github.com/taoliu/MACS/, [132]

Not available

2. ZINBA [131]

ATAC-seq

1. ZINBA [131]

1. Digital genomic footprinting algorithms [19, 78, 83, 85, 128, 146, 149]

2. MACS2; https://github.com/taoliu/MACS/, [132]

2. CENTIPEDE [151]

 

3. Hotspot, DNase2Hotspots [21, 130]