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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]