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CSU-KangHu / HiTE

High-precision TE Annotator
GNU General Public License v3.0
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Identify intact elements of a paticular TE type #4

Closed MrbrilliantLL closed 1 month ago

MrbrilliantLL commented 1 month ago

Hi! Thanks for the excellent tools!

How can I get the annotation of specified TE type (e.g. LTR or TIR)? Like the "Divide and conquer" part in EDTA pipeline. Many thanks!

CSU-KangHu commented 1 month ago

Hi @MrbrilliantLL ,

Currently, HiTE can only output all types of transposons, with different types of transposons being saved to separate files. For example, LTRs are found in the confident_ltr_cut.fa.cons file, TIRs in the confident_tir.fa file, and all types of transposons in the confident_TE.cons.fa file.

Thank you for your suggestion. We plan to implement a "Divide and conquer" feature similar to EDTA in the next update.

Best , Kang

MrbrilliantLL commented 1 month ago

Thanks for your timely response! Looking forward to the next version !!!

CSU-KangHu commented 1 month ago

Hi @MrbrilliantLL,

I just submitted a new commit. HiTE now supports the --te_type parameter to retrieve specific types of TE output, including ltr, tir, helitron, non-ltr, and all. I hope this is helpful for you. Note: Currently, this feature is only available in the Conda version of HiTE. The Singularity and Docker images will be updated with the next major release.

I will close this issue for now, but feel free to reopen it if you encounter any further problems.

Best regards,
Kang

MrbrilliantLL commented 1 month ago

Got it, thanks again for your help!