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TobyBaril / EarlGrey

Earl Grey: A fully automated TE curation and annotation pipeline
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Question: PanTE analyses for EarlGrey #147

Closed Chenglin20170390 closed 1 month ago

Chenglin20170390 commented 1 month ago

Hi , I am wondering whether EarlGrey can be used for panTE analysis. Of so, are there any relevant documents or pipelines for reference?

Bests, Lin

TobyBaril commented 1 month ago

Hi,

Are you trying to generate a single TE library from a pangenome? Or are you interested in using a pangenome to detect polymorphic insertions?

If the former, you can make libraries with Earl Grey, and then cluster these and annotate each genome of the pangenome with a given library.

If the latter, you might be better off looking at tools like Pantera or GraffiTE as these might be more what you are looking for!