Table 2.
Advantage and limitations of TEF
| Advantage and limitations | Algorithm 1 TSD method |
Algorithm 2 Junction method |
|---|---|---|
| Detect TE transposition without TE reference sequence | Yes | Yes |
| Detect TE transposition which does not make TSD during transposition or with broken TSD | No | No |
| Analyze single-end reads | Yes | Yes |
| Detect TE transposed in one sample | No | Yes |
| Detect only transposed TEs | Yes | Yes |
| Detect TE transposition without reference sequence | Yes | No |
| Detect TE transposition not in reference sequence | Yes | No |
| Always detect TE transposition from different combinations of samples | No | No |
| Detect TE excision | No | No |