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 |