Evaluation of methods to detect circular RNAs from single-end RNA-sequencing data

BMC Genomics

Table 1 Results of all circRNA detection methods for single-end and paired-end experimental RNA-Seq datasets across four cell lines. The columns Total, Non-dep, and Percent indicate the total detected circRNAs, the number of non-depleted circRNAs, and the proportion of the non-depleted RNAs respectively. Clirc and CircScan are not applicable to the paired-end datasets

Dataset	Method	Single-end			Paired-end
		Total	Non-dep	Percent	Total	Non-dep	Percent
HEK293	Ciri2	5841	3413	0.584	4397	3018	0.686
	CircExplorer	4138	2393	0.578	1999	1389	0.695
	DCC	2366	1389	0.587	301	193	0.641
	circRNA_finder	5015	2656	0.530	2244	1510	0.673
	find_circ2	4607	2899	0.629	4605	2897	0.629
	UROBORUS	469	293	0.625	840	453	0.539
	Clirc	0	0	0.000	.	.	.
	CircScan	970	578	0.596	.	.	.
HELA	Ciri2	7349	2981	0.406	6205	2885	0.465
	CircExplorer	5469	2010	0.368	2728	1362	0.499
	DCC	3704	1225	0.331	452	215	0.476
	circRNA_finder	7086	2255	0.318	3299	1520	0.461
	find_circ2	7529	2785	0.370	7520	2786	0.370
	UROBORUS	640	266	0.416	1469	473	0.322
	Clirc	136	37	0.272	.	.	.
	CircScan	2269	943	0.416	.	.	.
HS68	Ciri2	5331	3406	0.639	4818	3198	0.664
	CircExplorer	3950	2533	0.641	2683	1847	0.688
	DCC	3122	1492	0.478	1747	1066	0.610
	circRNA_finder	6402	2806	0.438	3520	2021	0.574
	find_circ2	9070	3395	0.374	9076	3404	0.375
	UROBORUS	551	356	0.646	1138	653	0.574
	Clirc	114	68	0.596	.	.	.
	CircScan	1727	1138	0.659	.	.	.
HEK293T	Ciri2	8486	1806	0.213	7719	1435	0.186
	CircExplorer	5347	1339	0.250	4102	679	0.166
	DCC	3896	750	0.193	2548	376	0.148
	circRNA_finder	8237	1521	0.185	4924	751	0.153
	find_circ2	11891	1783	0.150	11896	1783	0.150
	UROBORUS	794	157	0.197	1545	351	0.227
	Clirc	166	23	0.139	.	.	.
	CircScan	2080	648	0.312	.	.	.

ISSN: 1471-2164