Table 1

RNA-seq data used to test TopHat-Fusion

Data source

Sample ID

Read type

Fragment length

Read length

Number of fragments (or reads)


Edgren et al. [12]

BT474

Paired

100, 200

50

21,423,697

Edgren et al. [12]

SKBR3

Paired

100, 200

50

18,140,246

Edgren et al. [12]

KPL4

Paired

100

50

6,796,443

Edgren et al. [12]

MCF7

Paired

100

50

8,409,785

Maher et al. [11]

VCaP

Paired

300

50

16,894,522

Maher et al. [11]

UHR

Paired

300

50

25,294,164

Maher et al. [11]

UHR

Single

100

56,129,471


The data came from two studies, and included four samples from breast cancer cells (BT474, SKBR3, KPL4, MCF7), one prostate cancer cell line (VCaP), and two samples from the Universal Human Reference (UHR) cell line. For paired-end data, two reads were generated from each fragment; thus, the total number of reads is twice the number of fragments.

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

Open Data