Table 2 CircRNA program characteristics.

From: Extracellular circular RNA profiles in plasma and urine of healthy, male college athletes

Program

Aligner

Version

Paired-End Read Aware

Annotation Aware

Default Junction Overlap

Adjusted Junction Overlap

Reference

KNIFE

bowtie2

1.4

Yes

Yes

13 nt

18 nt

44

find_circ

bowtie2

1.0

No

No

18 nt

—

21

MapSplice

bowtie

2.1.8

Yes

Yes

10 nt

18 nt

45

CIRCexplorer

STAR

1.1.7

No*

Yes

15 nt**

18 nt

46

CIRI

bwa

2.0.1

Yes

Yes

19 nt***

—

47

DCC

STAR

0.3.2

Yes

Yes

15 nt**

18 nt

48

  1. *The latest version of CIRCexplorer now supports paired-end reads.
  2. **CIRCexplorer and DCC use the STAR chimeric junctions output, so the junction overlap for these tools is set by the splice junction parameters during STAR alignment.
  3. ***The default minimum seed length (k) for bwa mem is 19 nucleotides.
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