Datasets.

*The 48-bp reads in the NCBI SRA set have a 2 bp initial barcode that was trimmed, resulting in 46 bp reads.Datasets used for benchmark tests. For H. sapiens and P. falciparum, two times are given for TopHat. For H. sapiens, the longer time is with more sensitive settings, but the shorter time resulted in less than 5% fewer junctions at a similar specificity. For P. falciparum, the longer time is with more sensitive but less stringent settings whereas the shorter time is for the more stringent settings that resulted in significantly fewer junctions but with a much higher specificity.