NestTE out

[porkfan]

Hello Dr. Ou! I have a transposable element (TE) that was annotated using RepeatModeler, resulting in a complete 3.5kb CACTA_TIR_transposon. However, using the EDTA2 and the latest panEDTA pipeline, the annotation resulted in a 3kb Mutator-type transposon plus a 900bp Mutator_TIR_transposon. According to previous reports, there is mention of a 3.6kb CACTA-type transposon, but there has been no mention of the existence of a Mutator. Should I consider this as an annotation error or a new discovery (a Mutator inserted into the CACTA transposon)?

[oushujun]

Nested insertions are prevalent. You may use TEtrimmer to curate them. Shujun

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On Fri, Jul 26, 2024 at 5:24 AM porkfan ***@***.***> wrote: Hello Dr. Ou! I have a transposable element (TE) that was annotated using RepeatModeler, resulting in a complete 3.5kb CACTA_TIR_transposon. However, using the EDTA2 and the latest panEDTA pipeline, the annotation resulted in a 3kb Mutator-type transposon plus a 900bp Mutator_TIR_transposon. According to previous reports, there is mention of a 3.6kb CACTA-type transposon, but there has been no mention of the existence of a Mutator. Should I consider this as an annotation error or a new discovery (a Mutator inserted into the CACTA transposon)? — Reply to this email directly, view it on GitHub <#488>, or unsubscribe <https://github.com/notifications/unsubscribe-auth/ABNX4NCR2E5BXAVO6O5KXSTZOIIWNAVCNFSM6AAAAABLQE5BZ6VHI2DSMVQWIX3LMV43ASLTON2WKOZSGQZTCOBRGQ4TENA> . You are receiving this because you are subscribed to this thread.Message ID: ***@***.***>

[porkfan]

Thank you for your prompt reply. I've heard quite a few recommendations about this software recently. I'll go back and learn more about it!