Table 1 Experiment 2 RNA-Seq performance metrics reveal differences between library methods in rRNA and hemoglobin mRNA levels.

From: RNA-Seq of human whole blood: Evaluation of globin RNA depletion on Ribo-Zero library method

 

Alignment Metrics

Gene Counts

Blood Sample

Library Method

Technical Replicate

Total reads

rRNA ratea

Globin ratea

Total mapped

Duplicate rateb

Exonic ratec

Intergenic ratec

Total countsd

Globin

Ratee

C1

Ribo-Zero Globin

1

75,889,973

3.91%

0.46%

74,970,455

56.86%

46.49%

8.53%

26,940,402

0.03%

2

68,187,212

5.17%

0.47%

67,382,218

57.07%

45.93%

9.61%

23,852,287

0.02%

3

66,912,681

12.16%

0.79%

65,920,965

59.11%

43.00%

14.99%

21,312,218

0.02%

Ribo-Zero Gold

1

62,258,328

2.38%

14.17%

61,590,653

58.87%

53.62%

6.02%

23,277,919

23.70%

2

63,705,502

2.52%

14.04%

63,053,394

60.15%

52.83%

6.36%

23,427,822

23.31%

3

64,213,439

2.42%

13.99%

63,462,386

60.39%

52.82%

6.44%

23,582,022

23.29%

C2

Ribo-Zero Globin

1

61,117,132

17.19%

0.88%

59,981,781

60.00%

40.97%

18.55%

17,569,235

0.03%

2

66,744,713

16.27%

0.91%

65,499,404

62.22%

41.02%

17.84%

19,226,041

0.02%

3

62,514,672

30.89%

1.65%

60,682,926

71.18%

34.45%

28.66%

13,765,481

0.03%

Ribo-Zero Gold

1

64,728,692

4.01%

13.90%

63,842,383

60.71%

52.01%

7.69%

22,556,548

23.87%

2

67,886,975

2.97%

14.08%

67,119,332

60.32%

52.75%

6.86%

24,114,916

23.80%

3

66,636,958

4.33%

14.66%

65,293,327

62.61%

53.46%

8.14%

22,931,860

25.83%

  1. aEstimated % of total reads via independent alignment of reads to only rRNA and hemoglobin sequences; b% of mapped reads; c% of mapped non-duplicate reads14; duniquely mapped reads unambiguously assigned to one gene; e% of gene counts.
  2. Rates in bold text highlight elevated rRNA detection in the Ribo-Zero Globin (Globin-Zero) libraries and the high hemoglobin mRNA levels in the Ribo-Zero Gold (RZG) libraries.
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