Keeping all full-length transposons? about edta HOT 5 CLOSED

Hi @aderzelle,

Thanks for your suggestion. I am working with a functionality to retain all intact transposons identified by EDTA, which could be useful for people who want to study the biology of transposons. I think this is essentially what you are proposing. Currently, EDTA produces a non-redundant library for the whole-genome annotation purpose.

Best,
Shujun

from edta.

Hi @aderzelle ,

Sorry for the delay response. I have updated EDTA, it now also outputs intact TEs. Please try it out and let me know if there is any issues.

Best,
Shujun

from edta.

The current version provides outputs for full-length LTR, TIR, and Helitrons in both fasta and gff formats. (*.intact.fa and *.intact.fa.gff). Feel free to reopen this issue if you identify new problems or have any suggestions.

from edta.

Hello,
it works however LTR are in gff3 formats while the others are in gff2 format, which might create confusion in downstream analysis (though it's not a big deal of course but as a little improvement they could be in the same gff version).

from edta.

Dear @aderzelle,

Thank you for your suggestions. I have incorporated the intact TE annotation to the whole-genome TE annotation. Also, gff format of the final annotation is more consistent with each other. Now the *EDTA.TEanno.gff file contains both structural-based and homology-based annotations. Please check out the new release or the latest repository for more details.

Happy New Year!

Best,
Shujun

from edta.