Table 1.

Comparison of CPU usage and “rejection” rates of INSPEcT and SSRE. The same batch (subset of the data described above) were provided to both methods (implemented in R). The output size refers to the number of transcripts that can be processed by the method and the speed-up is the ratio of INSPEcT over SSRE transcript processing time. SSRE is about 42 times faster than INSPEcT with (0.8 ms vs 34 ms per processed transcript). However, SSRE also discards more transcripts than INSPEcT, providing rates for 38% of them vs 47% for INSPEcT. Those low numbers can be explained by the fact that many transcripts (especially non-coding ones) have a very low expression that is poorly estimated in the labeled RNA pool

Batch size	INSPEcT		SSRE		Speed-up
	Output size	CPU processing time [s] ([ms/transcript])	Output size	CPU processing time [s] ([ms/transcript])
10	5 (50%)	2.09 (402)	5 (50%)	0.052 (10)	40
1000	469 (47%)	15.889 (33)	387 (39%)	0.310 (0.8)	42
91702	42650 (47%)	1453.336 (34)	34512 (38%)	27.792 (0.8)	42