Table 2.

Summary of experimental, non-simulated datasets used in this study

Data source	Dataset	Cell line/tissue type	RNase R treated?	Number of reads	Number of mapped reads	Median
						insert size
SRA	SRR1636985	HeLa	Yes	26 619  490	24 370  337	200
	SRR1637089	HeLa	No	89 866 900	63 842 205	140
	SRR1636986	HeLa	Yes	47 011  426	42 027  801	200
	SRR1637090	HeLa	No	71 370 620	53 957 685	130
	SRR444974	Hs68	Yes	316 611  710	271 345  091	160
	SRR444655	Hs68	No	314 106 316	109 706 923	150
In-house	MG_1	MTG	Yes	107 609  934	96 300  242	150
generated	MG_5	MTG	No	96 215 516	86 315 844	150
	MG_2	MTG	Yes	96 840  790	86 560  619	150
	MG_6	MTG	No	101 609 754	90 750 108	150
	MG_3	MTG	Yes	111 576  344	100 264  691	150
	MG_7	MTG	No	111 314 114	98 894 498	150