TopHat-Fusion: an algorithm for discovery of novel fusion transcripts

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.

ISSN: 1474-760X