Combining existing TE library with EDTA results

[oushujun]

I think I closed this a bit too early, I do have a question that isn't discussed in #8. If we plan on including homology-based TEs from RepBase or Dfam as well as the structure-based TEs from EDTA, do you suggest including the RepBase/Dfam libraries in the -curatedlib option of the EDTA run? Or should we run EDTA and then concatenate with RepBase/Dfam results?

Originally posted by @Neato-Nick in #18 (comment)

[oushujun]

Hi @Neato-Nick:

Sorry I just saw your post under the closed issue.

If you have a TE library at hand and want to combine it with the EDTA library, then the -curatedlib option is your friend. However, you have to make sure the library you are providing is 100% trustworthy, because EDTA treats it as curated and true, so all sequence in the provided file will be retained in the final library, then EDTA will find novel sequences and add on it. If there are substantial false positives in the provided file, the final library will be low quality as well.

Best,
Shujun