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Table 1 A summary of comparing for the benchmark data with a bin size of 30 bp.

From: QChIPat: a quantitative method to identify distinct binding patterns for two biological ChIP-seq samples in different experimental conditions

Methods

H3K4me3

H3K36me3

H3K27me3

 

ESC enriched

NPC enriched

ESC enriched

NPC enriched

ESC enriched

NPC enriched

Linear normalization

5738 (87.9%)*

913 (61.4%)

779 (29.9%)

1403 (58.7%)

3483 (77.2%)

495 (50.9%)

NEB normalization

6912 (78.2%)

621 (71.3%)

951(25.6%)

1080 (70.8%)

3664 (72.3%)

428 (55.1%)

Quantile normalization

3918 (98.3%)

2611 (31.3%)

526 (43.3%)

1952 (35.9%)

2875 ( 85.8%)

793 (38.8%)

Non-normalization

6959 (78.2%)

680 (70.3%)

741 (31.4%)

1409 (58.5%)

3266 (79.7%)

519 (49.3%)

ChIPDiff

12975

1767

1157

1227

3832

888

  1. *Values in parentheses are percentage of DHMSs overlapping with ChIPDiff.