Table 4

Accuracies obtained from RNA-Seq data sets with various properties

Species

Seq. Error

Read type

Read length

Read number

(×106)

Throughput

(MB)

MPE

10% EF

FP


M

N

SE

35

20

700

3.1/4.2/7.1

13.7/25.0/44.0

1.0/1.8/10.9

M

N

SE

70

20

1400

3.1/4.1/6.0

13.6/23.9/40.4

0.8/1.5/8.2

M

N

PE

35

20

1400

3.0/3.9/4.9

13.3/21.9/34.2

1.1/1.8/13.4

M

N

SE

35

40

1400

2.3/3.1/4.8

8.4/18.5/35.8

0.7/1.3/10.5


M

Y

SE

35

20

700

3.1/4.2/6.9

14.1/25.2/43.0

1.1/1.9/13.2

M

Y

SE

70

20

1400

3.0/4.0/6.0

14.2/24.4/40.6

1.1/1.6/9.5

M

Y

PE

35

20

1400

3.0/3.9/5.1

14.0/22.9/35.5

1.3/1.9/12.1

M

Y

SE

35

40

1400

2.2/3.0/5.0

8.5/18.4/35.7

0.9/1.5/11.3


H

N

SE

35

20

700

4.0/7.8/14.3

20.2/43.5/58.6

3.6/8.0/21.6

H

N

SE

70

20

1400

3.9/7.3/11.9

19.3/41.0/54.4

3.5/7.0/17.3

H

N

PE

35

20

1400

3.7/6.2/9.0

17.0/36.4/47.3

3.7/6.4/14.0

H

N

SE

35

40

1400

2.9/5.7/10.1

13.4/35.4/50.3

2.7/6.3/20.3


H

Y

SE

35

20

700

3.9/7.7/14.8

19.5/43.2/59.3

3.9/8.1/20.8

H

Y

SE

70

20

1400

3.8/7.2/12.4

19.2/40.8/55.2

3.9/7.1/17.7

H

Y

PE

35

20

1400

3.8/6.5/9.2

19.0/37.8/48.2

4.2/6.4/13.9

H

Y

SE

35

40

1400

2.9/5.6/10.3

12.8/35.5/50.8

3.0/6.3/18.8


Accuracy of abundance estimates from RNA-Seq data sets varying in species (H = human, M = mouse), sequencing error, type (SE or PE) of reads, number of reads, and length of reads. Values are given as gene/global isoform/within-gene isoform.

Li and Dewey BMC Bioinformatics 2011 12:323   doi:10.1186/1471-2105-12-323

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