Table 5

Comparisons of TopHat-Fusion and deFuse for SKBR3 and MCF7 cell lines

TopHat-Fusion

deFuse

Sample ID

Fusion genes (left-right)

Chromosomes (left-right)

Spanning reads

Spanning pairs

Spanning reads

Spanning pairs


SKBR3

TATDN1-GSDMB

8-17

311

555

322

95

SKBR3

RARA-PKIA

17-8

1

5

1

4

SKBR3

ANKHD1-PCDH1

5-5

4

15

5

11

SKBR3

CCDC85C-SETD3

14-14

5

6

6

3

SKBR3

SUMF1-LRRFIP2

3-3

3

12

5

12

SKBR3

WDR67-ZNF704

8-8

3

3

3

2

SKBR3

CYTH1-EIF3H

17-8

18

37

16

27

MCF7

BCAS4-BCAS3

20-17

105

284

106

105

MCF7

ARFGEF2-SULF2

20-20

17

20

17

12

MCF7

RPS6KB1-TMEM49

17-17

4

3

6

2


Comparisons of the number of spanning reads and mate pairs reported by TopHat-Fusion and deFuse for ten previously reported fusion transcripts in the SKBR3 and MCF7 sample data.

Kim and Salzberg Genome Biology 2011 12:R72   doi:10.1186/gb-2011-12-8-r72

Open Data