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zhangrengang / TEsorter

TEsorter: an accurate and fast method to classify LTR-retrotransposons in plant genomes
https://doi.org/10.1093/hr/uhac017
GNU General Public License v3.0
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autonomous elements for TIR #33

Closed gorliver closed 1 year ago

gorliver commented 2 years ago

Hi Rengang @zhangrengang , Thank you for the useful tool! I'm seeking to classify DNA transposons and identify autonomous elements. In the output, it seems all the classified TIRs are unknown in the Complete collum, even with the TPase domains. Do you have any suggestions to identify the autonomous elements? Thanks!

zhangrengang commented 2 years ago

Hi @gorliver, The Complete collum is only designed for LTR elements, as LTRs contain multiple domains. For autonomous elements, you may reduce the rule 80-80-80 to e.g., 50-30-80 (80-80-80 aims to family-level classifications in its original literature, which seems to be too high for superfamily-level classifications; but we do not have a suitable criterion for superfamily-level classifications) or try other tools such as deepTE and RepeatClassifier.