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Table 1 The number of peaks called by different algorithms and at thresholds, and corresponding number of mapped genes

From: Improving ChIP-seq peak-calling for functional co-regulator binding by integrating multiple sources of biological information

Method

Total number of peaks

Number of genes mapped

MACS, p = 1E-8

1,966

996

MACS, p = 1E-5

4,678

2,054

MACS, p = 1E-3

23,306

6,341

T-PIC, p = 1E-3

4,453

1,676

T-PIC, p = 1E-2

6,598

2,318

BayesPeak (PP = 0.90)

15,622

4,495

BayesPeak (PP = 0.70)

21,373

5,507

BayesPeak (PP = 0.5)

27,990

6,533

Union*

38,324

8,057

Intersection*

4,811

2,029

  1. * Union and intersection of the peaks by the three methods, as shown in Figure 1.
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BMC Genomics

ISSN: 1471-2164

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