Table 1. Mapping and splicing statistics for paired-end runs.

Dataset	#Confidently Aligned Pairs	#Known Splice	#Putative Splice	#Putative Fusion
UHR-1	79,654,007	127,987	9,025	5
UHR-2	113,699,316	136,839	14,365	13
HBR-1	89,066,940	129,031	8,709	8
HBR-2	130,521,674	138,718	14,204	14
MCF-7-1	79,654,007	123,442	17,373	40
MCF-7-2	86,796,592	120,503	19,437	56

Notes: Confidently aligned pairs was defined as primary alignments with PQV>10. 120 and 150 refer to insert size of RNA library. MCF-7 and MCF-7 -2 libraries were prepared separately from the same lot. Known splicing events are found in RefSeq database whereas putative splicing events were not.