Table 4

Chimeric RNA detection in breast cancer libraries

Edgren

libraries

CRAC

TopHat-fusion

Raw

After GSNAP

Raw

After GSNAP

Number of chRNAs

Number of reads

Number of chRNAs

Number of reads

Number of chRNAs

Number of reads

Number of chRNAs

Number of reads


BT-474

692

9,661

153

460

109,711

349,801

81,327

189,523

KPL-4

407

5,157

60

199

32,412

98,330

23,075

53,165

MCF-7

466

3,475

90

180

42,738

121,544

27,267

57,676

SK-BR-3

703

9,354

152

577

86,249

241,219

61,494

130,682


TopHat-fusion reports approximately 200 times more raw candidates than CRAC; this ratio increases after filtering. Comparison with the set of validated chRNAs by Edgren et al. [27] shows that both the filtered and unfiltered predictions of CRAC and TopHat-fusion include respectively 20 and 21 true chRNAs and they agree for 17 of them.

Philippe et al. Genome Biology 2013 14:R30   doi:10.1186/gb-2013-14-3-r30

Open Data