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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

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

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   . . .