Table 2 Peak calling, sensitivity and specificity
From: A comparative study of ChIP-seq sequencing library preparation methods
Method | Input Amount (ng) | Mean number of peaks called | Mean number of reference peaks overlapped by sample peaks | Mean number of sample peaks not found in reference dataset | Mean sensitivity (% reference peaks detected) | Mean specificity (% method peaks found in reference dataset) |
|---|---|---|---|---|---|---|
PCR-free | 100 | 19 221 ± 157 | 17 124 ± 0 | 2 097 ± 157 | 100 % | 89 % |
Accel-2S | 1 | 18 190 ± 123 | 16 574 ± 38 | 1 616 ± 115 | 97 % | 91 % |
0.1 | 18 179 ± 124 | 16 505 ± 62 | 1 675 ± 103 | 96 % | 91 % | |
Bowman | 1 | 19 082 ± 334 | 16 096 ± 111 | 2 986 ± 228 | 94 % | 84 % |
0.1 | 18 986 ± 365 | 16 155 ± 48 | 2 831 ± 384 | 94 % | 85 % | |
SeqPlex | 1 | 21 382 ± 265 | 13 612 ± 78 | 7 770 ± 255 | 79 % | 64 % |
0.1 | 35 867 ± 3 861 | 13 905 ± 113 | 21 962 ± 3 902 | 81 % | 39 % | |
SMART | 1 | 17 906 ± 765 | 15 723 ± 99 | 2 182 ± 807 | 92 % | 88 % |
0.1 | 19 893 ± 3 196 | 15 622 ± 166 | 4 271 ± 3 349 | 91 % | 80 % | |
TELP | 1 | 20 529 ± 1 592 | 15 528 ± 81 | 5 001 ± 1 641 | 91 % | 76 % |
0.1 | 20 149 ± 1 619 | 15 370 ± 105 | 4 778 ± 1 683 | 90 % | 77 % | |
ThruPLEX | 1 | 18 377 ± 152 | 16 462 ± 36 | 1 916 ± 138 | 96 % | 90 % |
0.1 | 18 015 ± 178 | 16 298 ± 44 | 1 717 ± 200 | 95 % | 90 % |