Features
SpliceMap aligns RNA-seq reads to a reference genome in order to discover splicing junctions. It is at least as sensitive and specific as state-of-the art tools. Some major features of SpliceMap are
- Support for arbitrarily long uneven read lengths
- Optional filtering
- Reports the reliability of each junction
- Reports non-uniquely mapped coverage
- Outputs in SAM format for easy down-stream analysis
- High speed
- Better performance on sensitivity, specificity and running time compared to existing tools (Refer to the paper for details. However the current SpliceMap is newer than the one in the paper.)
- Includes developers who provide prompt responses to any of your questions!
- Outputs MD string in SAM file for SNP calling without a reference.
The following table gives an idea of the improvements expected from long-reads. The results are from the same 20 million 100bp RNA-seq reads cut to different lengths and mapped to the human genome (hg18). Specificity is calculated based on the number of junctions validated by ESTs. The results are unfiltered, improvements to specificity can be achieved using the optional filters.
| 50bp | 75bp | 100bp | |
| Total Junctions | 158,060 | 161,295 | 170,213 |
| EST Validated | 136,054 | 137,964 | 142,432 |
| Specificity | 86.08% | 85.54% | 83.68% |
SpliceMap 3.3.5.2