ChIPseqR: analysis of ChIP-seq experiments

BMC Bioinformatics

Table 1 Number of nucleosomes identified on simulated data by different methods at three levels of coverage

		ChIPseqR	GeneTrack	MSP	MTC	WTD
3 M reads	Sample 1	8,386	8,386*	4,809	0	0
	Sample 2	8,299	8,299*	4,726	0	4
	Sample 3	8,388	8,388*	4,892	0	0
	Total	25,073	25,073*	14,427	0	4
	% stable	24.9%	4.7%	5.4%	-	25%
	repeatability	0.07	0.02	0.007	-	-
6 M reads	Sample 1	6,257	6,257*	7,968	0	0
	Sample 2	6,286	6,286*	7,912	0	0
	Sample 3	6,431	6,431*	8,139	0	0
	Total	18,974	18,974*	24,019	0	0
	% stable	52.7%	6.7%	6.5%	-	-
	repeatability	0.16	0.05	0.014	-	-
10 M reads	Sample 1	19,907	19,907*	9,989	542	142
	Sample 2	20,359	20,359*	9,951	621	143
	Sample 3	20,223	20,223*	9,851	545	192
	Total	60,489	60,489*	29,791	1,708	477
	% stable	32.5%	18.2%	7.7%	68.1%	48.8%
	repeatability	0.31	0.16	0.06	0.10	0.04

*Cut-off was chosen to give the same number of significant predictions as ChIPseqR.
For each sample the number of predicted nucleosomes is reported. The total number of significant predictions for each level of coverage is reported together with the proportion of stable nucleosomes that were identified in all three samples as well as a measure of repeatability of stable nucleosome predictions between samples (see text for details).

ISSN: 1471-2105