Table 3.
Sequencing depth dependency and isoform annotation basis of the reviewed tools.
| Tool | Sequencing Depth Threshold | Isoform Annotation Dependency |
|---|---|---|
| Alt Event Finder | N/A | no |
| SpliceMap | 50X | no |
| FineSplice | N/A | no |
| RSW | N/A | no |
| RSR | N/A | no |
| PASTA | N/A | no |
| rMATS | N/A | yes |
| SOAPsplice | 10X | no |
| SplicePie | N/A | no |
| SplicingCompass | N/A | yes |
| TopHat | 20X | no |
| TrueSight | N/A | no |
| NSMAP | N/A | no |
| rSeqDiff | N/A | yes |
| rSeqNP | N/A | yes |
Note: Since there is no clear declaration of sequencing depth threshold values mentioned in some of the tool papers, the sequencing depth information in the depth threshold column is marked as “N/A”.