EDTA ,Transposon detection, repeat modeler and masker

Question

[manaswiniparija3]

I used EDTA to identify and annotate transposable elements (TE). it uses both structure-based and homology-based TE detection methods to identify known TEs. but in the homology-based TE detection method, both structurally intact (having complete jumping signatures) and fragmented and Dead TEs are detected. can anyone suggest how to identify and separate structurally intact and fragmented and Dead TEs in the result of homology-based detection methods?

[biofalconch]

I think this is out of the scope of these tools, really to know if a TE is structurally inact/dead I think you would need a little bit of knowledge on their biology and if they have all the elements intact within them

[manaswiniparija3]

ok, thanks for your reply