Modeling the next generation sequencing sample processing pipeline for the purposes of classification

BMC Bioinformatics

Table 3 Percentage of the NGS-reads experiments recovering certain number of global markers after feature selection for COV=0.05 and ρ =0 . 4

NGS-reads	Sample	<8	8	9	10
range	size	markers	markers	markers	markers
	n=60	99.64	0.34	0.02	0.00
1K-50K	n=120	69.98	20.48	8.64	0.90
	n=180	27.84	33.76	31.20	7.20
	n=60	77.30	16.54	5.60	0.56
50K-100K (SAGE-tags)	n=120	10.03	26.12	44.08	19.77
	n=180	0.88	7.53	39.10	52.49
	n=60	41.30	32.44	22.00	4.26
250K-300K	n=120	2.10	11.82	41.56	44.52
	n=180	0.10	1.74	22.88	75.28
	n=60	34.54	32.74	26.22	6.50
500K-550K	n=120	1.82	11.08	41.56	45.54
	n=180	0.10	1.56	20.26	78.08
	n=60	30.98	31.36	30.04	7.62
5M-5M+50K	n=120	1.24	8.72	37.56	52.48
	n=180	0.04	1.20	18.92	79.84
	n=60	29.74	32.68	29.16	8.42
10M-10M+50K	n=120	1.22	8.28	37.36	53.14
	n=180	0.04	1.00	18.84	80.12
	n=60	28.96	33.16	29.92	7.96
15M-15M+50K	n=120	1.06	8.06	38.38	52.50
	n=180	0.06	1.36	18.08	80.50
	n=60	28.90	32.36	30.38	8.36
25M-25M+50K	n=120	0.98	8.00	40.12	50.90
	n=180	0.06	1.14	17.68	81.12
	n=60	28.60	32.50	30.42	8.48
32.5M-32.5M+50K	n=120	1.10	7.48	39.02	52.40
	n=180	0.02	1.02	17.80	81.16
	n=60	30.20	31.46	29.40	8.94
40M-40M+50K	n=120	1.34	8.50	38.12	52.04
	n=180	0.08	1.02	18.62	80.28
	n=60	28.84	32.18	30.32	8.66
50M-50M+50K	n=120	1.22	8.46	39.02	51.30
	n=180	0.04	1.28	17.24	81.44
	n=60	29.12	32.50	29.72	8.66
75M-75M+50K	n=120	1.08	7.98	39.64	51.30
	n=180	0.02	1.16	17.14	81.68
	n=60	29.14	32.16	30.84	7.86
100M-100M+50K	n=120	1.22	8.78	39.10	50.90
	n=180	0.08	1.22	18.32	80.38

ISSN: 1471-2105