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TobyBaril / EarlGrey

Earl Grey: A fully automated TE curation and annotation pipeline
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Gff3 Question #127

Closed sherlock0088 closed 3 months ago

sherlock0088 commented 3 months ago

Hi,

Thank you for providing this great pipeline! It is very useful on my TE analysis! Especially kimura distance function.

However, I have a small question related to TE gff3 annotation file. What are the tstart and tend in the gff3 files? are they related to the physical start and end of TE?

Best, Yupeng

TobyBaril commented 3 months ago

Hi Yupeng,

Thanks for checking out Earl Grey! The TSTART and TEND coordinates are used by RepeatCraft in the defragmentation step, and refer to the coordinates in the consensus sequence that match the genome annotation. For example, if there is a partial element in the genome, these coordinates will tell you which parts of the consensus sequence match.

Best wishes,

Toby