Many overlapping regions of TE

oushujun / EDTA

Extensive de-novo TE Annotator

https://genomebiology.biomedcentral.com/articles/10.1186/s13059-019-1905-y

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Many overlapping regions of TE #384

Closed XXboop closed 8 months ago

XXboop commented 9 months ago

Dear Dr.Ou

I used EDTA v2.01 to identify TE. but in the genome.fasta.mod.EDTA.TEanno.gff3 check found that there are very many TE overlap regions. As shown below. Do I need to process and filter these overlapping TE? Because I want to do a detailed analysis of TE in this genome. Thanks very much!

Best regards

oushujun commented 9 months ago

Hello,

Sorry for the delay. Please check out the wiki to better understand the output gff file. Also, naturally nested structures are prevalent. Misannotations are also likely for cases like tandem repeats.

Shujun